Variant report

Variant	rs12023892
Chromosome Location	chr1:169338326-169338327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:169336275-169338640	MCF10A-Er-Src	breast:	n/a	n/a
2	HCFC1	chr1:169336279-169338667	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr1:169336053-169338642	IMR90	lung:	n/a	n/a
4	MXI1	chr1:169336098-169338754	SK-N-SH	brain:	n/a	n/a
5	GABPA	chr1:169336412-169338346	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:169338281-169338331	Jurkat	blood:	n/a
2	chr1:169338281-169338331	HEK293	kidney:	embryo
3	chr1:169338281-169338331	MCF10A-Er-Src	breast:	n/a
4	chr1:169338281-169338331	H1-hESC	embryonic stem cell:	embryo
5	chr1:169338281-169338331	GM12878	blood:	n/a
6	chr1:169338281-169338331	SK-N-MC	brain:	n/a
7	chr1:169338281-169338331	BE2_C	brain:	n/a
8	chr1:169338281-169338331	GM06990	blood:	n/a
9	chr1:169338281-169338331	T-47D	breast:	n/a
10	chr1:169338281-169338331	HAEpiC	amniotic membrane:	n/a
11	chr1:169338281-169338331	AG10803	skin:	n/a
12	chr1:169338281-169338331	HNPCEpiC	eye:	n/a
13	chr1:169338281-169338331	HUVEC	blood vessel:	n/a
14	chr1:169338281-169338331	NT2-D1	testis:	n/a
15	chr1:169338281-169338331	BJ	skin:	n/a
16	chr1:169338281-169338331	CMK	blood:	n/a
17	chr1:169338281-169338331	ProgFib	skin:	n/a
18	chr1:169338281-169338331	HepG2	liver:	n/a
19	chr1:169338281-169338331	SKMC	muscle:	n/a
20	chr1:169338281-169338331	IMR90	lung:	fetal
21	chr1:169338281-169338331	HCF	heart:	n/a
22	chr1:169338281-169338331	NH-A	brain:	n/a
23	chr1:169338281-169338331	GM12892	blood:	n/a
24	chr1:169338281-169338331	ECC-1	luminal epithelium:	n/a
25	chr1:169338281-169338331	AG04450	lung:	fetal
26	chr1:169338281-169338331	RPTEC	kidney:	n/a
27	chr1:169338281-169338331	HL-60	blood:	n/a
28	chr1:169338281-169338331	GM19239	blood:	n/a
29	chr1:169338281-169338331	K562	blood:	n/a
30	chr1:169338281-169338331	NB4	blood:	n/a
31	chr1:169338281-169338331	HEEpiC	esophagus:	n/a
32	chr1:169338281-169338331	AoSMC	blood vessel:	n/a
33	chr1:169338281-169338331	NHBE	bronchial:	n/a
34	chr1:169338281-169338331	Hepatocyte	liver:	n/a
35	chr1:169338281-169338331	HCT-116	colon:	n/a
36	chr1:169338281-169338331	HRPEpiC	eye:	n/a
37	chr1:169338281-169338331	HMEC	breast:	n/a
38	chr1:169338281-169338331	LNCaP	prostate:	n/a
39	chr1:169338281-169338331	AG09309	skin:	n/a
40	chr1:169338281-169338331	ovcar-3	ovarian:	n/a
41	chr1:169338281-169338331	U87	brain:	n/a
42	chr1:169338281-169338331	HCPEpiC	choroid plexus:	n/a
43	chr1:169338281-169338331	MCF-7	breast:	n/a
44	chr1:169338281-169338331	PANC-1	pancreas:	n/a
45	chr1:169338281-169338331	AG09319	gingival:	n/a
46	chr1:169338281-169338331	HRCEpiC	kidney:	n/a
47	chr1:169338281-169338331	Caco-2	colon:	n/a
48	chr1:169338281-169338331	AG04449	skin:	fetal
49	chr1:169338281-169338331	NHDF-neo	bronchial:	n/a
50	chr1:169338281-169338331	SAEC	small airway:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169337822..169339719-chr1:169451874..169454199,3	K562	blood:
2	chr1:169075479..169078672-chr1:169335264..169338570,4	MCF-7	breast:
3	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
4	chr1:169338121..169342264-chr1:169451874..169455112,4	K562	blood:
5	chr1:169338197..169339910-chr1:169345261..169347920,2	MCF-7	breast:

No data

Variant related genes	Relation type
NME7	TF binding region
NME7	CpG island
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10489187	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489188	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800439	0.81[ASN][1000 genomes]
rs10919146	0.95[EUR][1000 genomes]
rs10919155	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919163	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799936	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799948	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11800843	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11808015	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11809378	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12021770	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023025	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023117	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026728	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12028813	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12030320	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12032201	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12033253	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12049227	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12239720	0.81[ASN][1000 genomes]
rs1400838	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517748	0.81[ASN][1000 genomes]
rs16862118	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16862172	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1980198	0.81[ASN][1000 genomes]
rs2235195	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2275299	0.81[ASN][1000 genomes]
rs28566091	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35269183	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818844	0.81[ASN][1000 genomes]
rs4656670	0.81[ASN][1000 genomes]
rs56859218	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61807018	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808977	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61808978	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61808980	0.81[ASN][1000 genomes]
rs6427191	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656923	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690801	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72702156	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72702179	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72702188	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535788	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554703	0.97[ASN][1000 genomes]
rs9659035	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169335800-169338400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:169335800-169338400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:169335800-169338400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:169335800-169338600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:169335800-169338600	Active TSS	K562	blood
6	chr1:169335800-169339000	Active TSS	NHLF	lung
7	chr1:169336000-169338400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:169336000-169338600	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:169336000-169339000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:169336200-169338400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:169336200-169338400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:169336200-169338400	Active TSS	A549	lung
13	chr1:169336200-169338600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:169336200-169338600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:169336200-169338600	Active TSS	Fetal Kidney	kidney
16	chr1:169336200-169339000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:169336200-169339200	Active TSS	HMEC	breast
18	chr1:169336400-169338400	Active TSS	H1 Cell Line	embryonic stem cell
19	chr1:169336400-169338400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:169336400-169338400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr1:169336400-169338400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:169336400-169338400	Active TSS	Brain Germinal Matrix	brain
23	chr1:169336400-169338400	Active TSS	Fetal Intestine Small	intestine
24	chr1:169336400-169338400	Active TSS	Right Ventricle	heart
25	chr1:169336400-169338400	Active TSS	HSMMtube	muscle
26	chr1:169336400-169338400	Active TSS	NHDF-Ad	bronchial
27	chr1:169336400-169338600	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:169336400-169338600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:169336400-169338600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:169336400-169338600	Active TSS	Right Atrium	heart
31	chr1:169336600-169338400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:169336600-169338400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:169336600-169338400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr1:169336600-169338400	ZNF genes & repeats	Fetal Brain Male	brain
35	chr1:169336600-169338400	Active TSS	Fetal Intestine Large	intestine
36	chr1:169336600-169338400	Active TSS	Fetal Muscle Leg	muscle
37	chr1:169336600-169338400	Active TSS	Fetal Stomach	stomach
38	chr1:169336600-169338400	Active TSS	GM12878-XiMat	blood
39	chr1:169336600-169338600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:169336600-169338600	Active TSS	Aorta	Aorta
41	chr1:169336600-169338600	Active TSS	Psoas Muscle	Psoas
42	chr1:169336600-169338800	Active TSS	Stomach Smooth Muscle	stomach
43	chr1:169336600-169338800	Active TSS	NHEK	skin
44	chr1:169336600-169339000	Active TSS	NH-A	brain
45	chr1:169336800-169338400	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr1:169336800-169338400	Active TSS	Hela-S3	cervix
47	chr1:169336800-169338400	Active TSS	HUVEC	blood vessel
48	chr1:169336800-169338600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:169336800-169338600	Active TSS	Fetal Thymus	thymus
50	chr1:169336800-169338600	Active TSS	Rectal Smooth Muscle	rectum

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