Variant report

Variant	rs549995739
Chromosome Location	chr1:213030404-213030405
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:213029909-213032745	GM12891	blood:	n/a	n/a
2	JUND	chr1:213030403-213030538	K562	blood:	n/a	n/a
3	POLR2A	chr1:213030204-213032910	K562	blood:	n/a	n/a
4	POLR2A	chr1:213029989-213032779	GM12878	blood:	n/a	n/a
5	GTF3C2	chr1:213030159-213031388	K562	blood:	n/a	n/a
6	JUN	chr1:213030281-213032721	K562	blood:	n/a	chr1:213031526-213031535 chr1:213031462-213031471

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:213030372-213030422	NH-A	brain:	n/a
2	chr1:213030372-213030422	Jurkat	blood:	n/a
3	chr1:213030372-213030422	AoSMC	blood vessel:	n/a
4	chr1:213030372-213030422	HepG2	liver:	n/a
5	chr1:213030372-213030422	SKMC	muscle:	n/a
6	chr1:213030372-213030422	MCF-7	breast:	n/a
7	chr1:213030372-213030422	GM12891	blood:	n/a
8	chr1:213030372-213030422	Caco-2	colon:	n/a
9	chr1:213030372-213030422	HRE	kidney:	n/a
10	chr1:213030372-213030422	HNPCEpiC	eye:	n/a
11	chr1:213030372-213030422	HCPEpiC	choroid plexus:	n/a
12	chr1:213030372-213030422	GM06990	blood:	n/a
13	chr1:213030372-213030422	SK-N-SH	brain:	n/a
14	chr1:213030372-213030422	GM12878	blood:	n/a
15	chr1:213030372-213030422	LNCaP	prostate:	n/a
16	chr1:213030372-213030422	GM19239	blood:	n/a
17	chr1:213030372-213030422	ovcar-3	ovarian:	n/a
18	chr1:213030372-213030422	IMR90	lung:	fetal
19	chr1:213030372-213030422	HMEC	breast:	n/a
20	chr1:213030372-213030422	HL-60	blood:	n/a
21	chr1:213030372-213030422	ECC-1	luminal epithelium:	n/a
22	chr1:213030372-213030422	HPAEpiC	pulmonary alveolar:	n/a
23	chr1:213030372-213030422	NHDF-neo	bronchial:	n/a
24	chr1:213030372-213030422	SAEC	small airway:	n/a
25	chr1:213030372-213030422	AG10803	skin:	n/a
26	chr1:213030372-213030422	RPTEC	kidney:	n/a
27	chr1:213030372-213030422	AG09309	skin:	n/a
28	chr1:213030372-213030422	AG04449	skin:	fetal
29	chr1:213030372-213030422	A549	lung:	n/a
30	chr1:213030372-213030422	CMK	blood:	n/a
31	chr1:213030372-213030422	ProgFib	skin:	n/a
32	chr1:213030372-213030422	HCM	heart:	n/a
33	chr1:213030372-213030422	Hela-S3	cervix:	n/a
34	chr1:213030372-213030422	PrEC	prostate:	n/a
35	chr1:213030372-213030422	SK-N-SH_RA	brain:	n/a
36	chr1:213030372-213030422	HCT-116	colon:	n/a
37	chr1:213030372-213030422	K562	blood:	n/a
38	chr1:213030372-213030422	HCF	heart:	n/a
39	chr1:213030372-213030422	AG09319	gingival:	n/a
40	chr1:213030372-213030422	HEK293	kidney:	embryo
41	chr1:213030372-213030422	BJ	skin:	n/a
42	chr1:213030372-213030422	U87	brain:	n/a
43	chr1:213030372-213030422	T-47D	breast:	n/a
44	chr1:213030372-213030422	NT2-D1	testis:	n/a
45	chr1:213030372-213030422	Hepatocyte	liver:	n/a
46	chr1:213030372-213030422	GM12892	blood:	n/a
47	chr1:213030372-213030422	H1-hESC	embryonic stem cell:	embryo
48	chr1:213030372-213030422	HAEpiC	amniotic membrane:	n/a
49	chr1:213030372-213030422	MCF10A-Er-Src	breast:	n/a
50	chr1:213030372-213030422	SK-N-MC	brain:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:213026064..213028809-chr1:213029690..213032627,2	K562	blood:
2	chr1:213025871..213028763-chr1:213030169..213033277,3	MCF-7	breast:
3	chr1:213025489..213028696-chr1:213029248..213033184,3	K562	blood:
4	chr1:212779176..212786217-chr1:213030148..213034937,8	K562	blood:
5	chr1:213030101..213032938-chr1:213186047..213190102,3	K562	blood:
6	chr1:213019184..213021421-chr1:213029036..213031526,2	K562	blood:
7	chr1:212965176..212966735-chr1:213030010..213031816,2	K562	blood:
8	chr1:212963280..212966676-chr1:213030010..213031803,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf227-1	chr1:213029946-213030514	ENSG00000198468
2	lnc-C1orf227-1	chr1:213029946-213030514	NONHSAT009411

No data

Variant related genes	Relation type
ENSG00000236317	TF binding region
FLVCR1	TF binding region
FLVCR1	CpG island
ENSG00000236317	CpG island
ENSG00000185523	Chromatin interaction
ENSG00000174606	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000236317	Chromatin interaction
ENSG00000117697	Chromatin interaction
ENSG00000235182	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv998261	chr1:213029814-213064209	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv998979	chr1:213029814-213073013	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213026200-213030800	Weak transcription	Thymus	Thymus
2	chr1:213027600-213030600	Weak transcription	HSMMtube	muscle
3	chr1:213028800-213030800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:213029600-213030600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:213029600-213033200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:213029600-213033400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:213029800-213030600	Enhancers	Brain Hippocampus Middle	brain
8	chr1:213029800-213030800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:213029800-213030800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:213029800-213032000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:213030000-213030600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr1:213030000-213030600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:213030000-213030600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:213030000-213030600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:213030000-213030600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:213030000-213030600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:213030000-213030600	Enhancers	Fetal Muscle Trunk	muscle
18	chr1:213030000-213030600	Enhancers	Left Ventricle	heart
19	chr1:213030000-213030600	Flanking Active TSS	A549	lung
20	chr1:213030000-213030600	Flanking Active TSS	GM12878-XiMat	blood
21	chr1:213030000-213030600	Flanking Active TSS	HepG2	liver
22	chr1:213030000-213030800	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:213030000-213030800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:213030000-213030800	Enhancers	Colonic Mucosa	Colon
25	chr1:213030000-213031000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr1:213030000-213031200	Flanking Active TSS	Dnd41	blood
27	chr1:213030000-213032800	Active TSS	Rectal Smooth Muscle	rectum
28	chr1:213030200-213030600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:213030200-213030600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:213030200-213030600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:213030200-213030600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:213030200-213030600	Enhancers	Primary hematopoietic stem cells	blood
33	chr1:213030200-213030600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:213030200-213030600	Enhancers	Fetal Brain Female	brain
35	chr1:213030200-213030600	Enhancers	Fetal Kidney	kidney
36	chr1:213030200-213030600	Enhancers	Fetal Muscle Leg	muscle
37	chr1:213030200-213030800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr1:213030200-213030800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:213030200-213030800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr1:213030200-213030800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:213030200-213030800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:213030200-213030800	Enhancers	Primary T cells from cord blood	blood
43	chr1:213030200-213030800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:213030200-213030800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:213030200-213030800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:213030200-213030800	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr1:213030200-213030800	Enhancers	Fetal Stomach	stomach
48	chr1:213030200-213030800	Enhancers	Lung	lung
49	chr1:213030200-213030800	Enhancers	Pancreas	Pancrea
50	chr1:213030200-213030800	Enhancers	Small Intestine	intestine

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