Variant report

Variant	rs56019647
Chromosome Location	chr1:153652129-153652130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:116)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:116 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:153651027-153652501	HepG2	liver:	n/a	n/a
2	CTCF	chr1:153649966-153652441	SK-N-SH	brain:	n/a	chr1:153650334-153650350 chr1:153650333-153650351 chr1:153650335-153650356
3	CTCF	chr1:153652020-153652170	GM12870	blood:	n/a	n/a
4	SIN3A	chr1:153650093-153653005	H1-hESC	embryonic stem cell:	n/a	chr1:153650997-153651008 chr1:153651070-153651081
5	CTCF	chr1:153652120-153652270	HEEpiC	esophagus:	n/a	n/a
6	CTCF	chr1:153652072-153652183	GM13977	blood:	n/a	n/a
7	CTCF	chr1:153652000-153652150	GM12871	blood:	n/a	n/a
8	CTBP2	chr1:153650221-153652352	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr1:153652080-153652230	GM12869	blood:	n/a	n/a
10	CTCF	chr1:153652000-153652150	GM12869	blood:	n/a	n/a
11	CTCF	chr1:153652060-153652210	HAc	cerebellar:	n/a	n/a
12	CTCF	chr1:153652080-153652230	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr1:153652040-153652190	GM12871	blood:	n/a	n/a
14	CTCF	chr1:153652020-153652170	AG09309	skin:	n/a	n/a
15	CTCF	chr1:153652080-153652230	HMEC	breast:	n/a	n/a
16	CTCF	chr1:153652060-153652210	HFF-Myc	foreskin:	n/a	n/a
17	CTCF	chr1:153651819-153652257	GM19238	blood:	n/a	n/a
18	CTCF	chr1:153652040-153652190	HCM	heart:	n/a	n/a
19	CTCF	chr1:153652124-153652263	Pancreas_OC	pancreas:	n/a	n/a
20	E2F6	chr1:153651977-153652174	K562	blood:	n/a	n/a
21	CTCF	chr1:153652040-153652190	HepG2	liver:	n/a	n/a
22	RAD21	chr1:153651936-153652212	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr1:153652060-153652210	GM12873	blood:	n/a	n/a
24	CTCF	chr1:153652040-153652190	GM12872	blood:	n/a	n/a
25	CTCF	chr1:153652100-153652250	HPAF	blood vessel:	n/a	n/a
26	CTCF	chr1:153651794-153652326	GM12878	blood:	n/a	n/a
27	CTCF	chr1:153652020-153652170	GM12878	blood:	n/a	n/a
28	CTCF	chr1:153652086-153652182	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr1:153652100-153652250	GM12867	blood:	n/a	n/a
30	CTCF	chr1:153652020-153652170	HFF	foreskin:	n/a	n/a
31	CTCF	chr1:153652080-153652230	GM12870	blood:	n/a	n/a
32	CTCF	chr1:153652040-153652190	WERI-Rb-1	eye:	n/a	n/a
33	CTCF	chr1:153652121-153652142	NHEK	skin:	n/a	n/a
34	MAX	chr1:153650983-153652510	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr1:153652080-153652230	HPAF	blood vessel:	n/a	n/a
36	MAX	chr1:153651966-153652319	K562	blood:	n/a	n/a
37	CTCF	chr1:153651718-153652288	K562	blood:	n/a	n/a
38	CTCF	chr1:153652060-153652210	HMF	breast:	n/a	n/a
39	CTCF	chr1:153652084-153652136	Spleen_OC	spleen:	n/a	n/a
40	CTCF	chr1:153652120-153652270	AG10803	skin:	n/a	n/a
41	CTCF	chr1:153652100-153652250	GM12872	blood:	n/a	n/a
42	E2F6	chr1:153651704-153652556	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr1:153652060-153652210	HBMEC	blood vessel:	n/a	n/a
44	CTCF	chr1:153652115-153652176	Fibrobl	skin:	n/a	n/a
45	CTCF	chr1:153652020-153652170	AG10803	skin:	n/a	n/a
46	CTCF	chr1:153651639-153652358	GM19239	blood:	n/a	n/a
47	MXI1	chr1:153652030-153652225	GM12878	blood:	n/a	n/a
48	CTCF	chr1:153652100-153652250	BJ	skin:	n/a	n/a
49	CTCF	chr1:153652100-153652250	HRE	kidney:	n/a	n/a
50	CTCF	chr1:153652080-153652230	GM12875	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153652122-153652172	ProgFib	skin:	n/a
2	chr1:153652122-153652172	Jurkat	blood:	n/a
3	chr1:153652122-153652172	H1-hESC	embryonic stem cell:	embryo
4	chr1:153652122-153652172	CMK	blood:	n/a
5	chr1:153652122-153652172	HEEpiC	esophagus:	n/a
6	chr1:153652122-153652172	GM12891	blood:	n/a
7	chr1:153652122-153652172	HEK293	kidney:	embryo
8	chr1:153652122-153652172	SKMC	muscle:	n/a
9	chr1:153652122-153652172	Hela-S3	cervix:	n/a
10	chr1:153652122-153652172	HAEpiC	amniotic membrane:	n/a
11	chr1:153652122-153652172	MCF10A-Er-Src	breast:	n/a
12	chr1:153652122-153652172	HUVEC	blood vessel:	n/a
13	chr1:153652122-153652172	A549	lung:	n/a
14	chr1:153652122-153652172	NHDF-neo	bronchial:	n/a
15	chr1:153652122-153652172	HPAEpiC	pulmonary alveolar:	n/a
16	chr1:153652122-153652172	LNCaP	prostate:	n/a
17	chr1:153652122-153652172	ECC-1	luminal epithelium:	n/a
18	chr1:153652122-153652172	PrEC	prostate:	n/a
19	chr1:153652122-153652172	GM12892	blood:	n/a
20	chr1:153652122-153652172	BE2_C	brain:	n/a
21	chr1:153652122-153652172	NB4	blood:	n/a
22	chr1:153652122-153652172	HCT-116	colon:	n/a
23	chr1:153652122-153652172	U87	brain:	n/a
24	chr1:153652122-153652172	SK-N-MC	brain:	n/a
25	chr1:153652122-153652172	PFSK-1	brain:	n/a
26	chr1:153652122-153652172	HRE	kidney:	n/a
27	chr1:153652122-153652172	GM12878	blood:	n/a
28	chr1:153652122-153652172	HL-60	blood:	n/a
29	chr1:153652122-153652172	AG04450	lung:	fetal
30	chr1:153652122-153652172	SK-N-SH	brain:	n/a
31	chr1:153652122-153652172	SAEC	small airway:	n/a
32	chr1:153652122-153652172	PANC-1	pancreas:	n/a
33	chr1:153652122-153652172	HCPEpiC	choroid plexus:	n/a
34	chr1:153652122-153652172	SK-N-SH_RA	brain:	n/a
35	chr1:153652122-153652172	HCM	heart:	n/a
36	chr1:153652122-153652172	AG04449	skin:	fetal
37	chr1:153652122-153652172	IMR90	lung:	fetal
38	chr1:153652122-153652172	BJ	skin:	n/a
39	chr1:153652122-153652172	HepG2	liver:	n/a
40	chr1:153652122-153652172	HRPEpiC	eye:	n/a
41	chr1:153652122-153652172	GM06990	blood:	n/a
42	chr1:153652122-153652172	Caco-2	colon:	n/a
43	chr1:153652122-153652172	AoSMC	blood vessel:	n/a
44	chr1:153652122-153652172	HRCEpiC	kidney:	n/a
45	chr1:153652122-153652172	AG09319	gingival:	n/a
46	chr1:153652122-153652172	AG09309	skin:	n/a
47	chr1:153652122-153652172	NT2-D1	testis:	n/a
48	chr1:153652122-153652172	HIPEpiC	eye:	n/a
49	chr1:153652122-153652172	HCF	heart:	n/a
50	chr1:153652122-153652172	HMEC	breast:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153651109..153660855-chr1:153698392..153702896,14	MCF-7	breast:
2	chr1:153650787..153653048-chr1:153700479..153702624,2	K562	blood:
3	chr1:153651404..153652981-chr1:153702351..153704100,2	MCF-7	breast:
4	chr1:153641478..153645789-chr1:153651108..153654010,4	K562	blood:
5	chr1:153651880..153654749-chr1:153747881..153749756,2	MCF-7	breast:
6	chr1:153651116..153652910-chr1:153740976..153746594,4	MCF-7	breast:
7	chr1:153652004..153654217-chr1:153745758..153747753,2	K562	blood:
8	chr1:153651747..153653331-chr1:153699938..153702201,2	MCF-7	breast:
9	chr1:153640859..153647825-chr1:153650423..153657512,10	K562	blood:
10	chr1:153651029..153654025-chr1:153963195..153965197,2	MCF-7	breast:

No data

Variant related genes	Relation type
NPR1	TF binding region
NPR1	CpG island
ENSG00000143621	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16835516	1.00[AMR][1000 genomes]
rs16835525	1.00[AMR][1000 genomes]
rs2228581	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2229835	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28730727	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153650000-153652400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
2	chr1:153650000-153653200	Active TSS	Fetal Kidney	kidney
3	chr1:153650200-153652400	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr1:153650200-153652400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
5	chr1:153650200-153652600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:153650200-153652800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:153650400-153652400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
8	chr1:153650400-153652400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
9	chr1:153650400-153652400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
10	chr1:153650400-153652400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
11	chr1:153650400-153652400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
12	chr1:153650400-153652400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
13	chr1:153650400-153652600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:153650400-153652600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr1:153650400-153653000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:153650400-153653200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:153650400-153653400	Active TSS	Aorta	Aorta
18	chr1:153650600-153652200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:153650600-153652400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:153650600-153652400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:153650600-153652400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:153650600-153652400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:153650600-153652400	Flanking Active TSS	Right Ventricle	heart
24	chr1:153650600-153652400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
25	chr1:153650600-153652400	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr1:153650600-153652400	Flanking Bivalent TSS/Enh	NHLF	lung
27	chr1:153650600-153652600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:153650600-153652600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:153650600-153652600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
30	chr1:153650600-153652600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:153650600-153652600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
32	chr1:153650600-153652600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:153650600-153652800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:153650600-153652800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:153650600-153653200	Active TSS	Left Ventricle	heart
36	chr1:153650600-153653400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:153650800-153652200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
38	chr1:153650800-153652200	Transcr. at gene 5' and 3'	Right Atrium	heart
39	chr1:153650800-153652400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr1:153650800-153652400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:153650800-153652400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:153650800-153652400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
43	chr1:153650800-153652400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
44	chr1:153650800-153652400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
45	chr1:153650800-153652400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:153650800-153652400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:153650800-153652400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:153650800-153652400	Flanking Active TSS	Gastric	stomach
49	chr1:153650800-153652400	Flanking Bivalent TSS/Enh	HMEC	breast
50	chr1:153650800-153652600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain

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