Variant report

Variant	rs2025431
Chromosome Location	chr6:37790385-37790386
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:37790275-37791051	GM12878	blood:	n/a	n/a
2	GATA1	chr6:37790217-37791654	K562	blood:	n/a	chr6:37791124-37791131
3	POLR2A	chr6:37790243-37791225	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:37790138..37792445-chr6:37803004..37804688,2	MCF-7	breast:
2	chr6:37788598..37791926-chr6:37799655..37801709,3	K562	blood:
3	chr6:37787991..37789516-chr6:37789518..37791025,2	MCF-7	breast:
4	chr6:37788588..37790791-chr6:37827723..37829422,2	MCF-7	breast:
5	chr6:37788608..37792008-chr6:37826692..37829268,3	K562	blood:
6	chr6:37785884..37787754-chr6:37789028..37791294,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225945	TF binding region
ENSG00000156639	Chromatin interaction
ENSG00000243313	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10428769	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10485030	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947702	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947704	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11751781	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11751927	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11751962	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11752521	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11752809	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11752814	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11753300	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11755095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755629	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11756713	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11757161	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11759458	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11759496	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11759826	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11967129	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969988	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12660919	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12661378	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661702	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12662426	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12664091	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12664768	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13190751	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13195545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13205214	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13205311	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13206035	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16890177	0.82[ASN][1000 genomes]
rs16890181	0.82[ASN][1000 genomes]
rs16890185	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16890267	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2064795	0.82[ASN][1000 genomes]
rs2103950	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2273441	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2274090	0.82[ASN][1000 genomes]
rs2274091	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2395689	0.81[ASN][1000 genomes]
rs2645111	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2645125	0.85[AMR][1000 genomes]
rs2645130	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2842510	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2842511	0.81[ASN][1000 genomes]
rs2842512	0.81[ASN][1000 genomes]
rs2842521	0.85[AMR][1000 genomes]
rs34254045	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34450348	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35122358	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35216205	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35772972	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35849984	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3844314	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55679841	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55996712	0.81[AMR][1000 genomes]
rs56023538	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56129320	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56177150	0.81[AMR][1000 genomes]
rs57198506	0.82[ASN][1000 genomes]
rs57402213	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58333612	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58611435	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58692659	0.80[ASN][1000 genomes]
rs59649654	0.82[ASN][1000 genomes]
rs60141491	0.82[ASN][1000 genomes]
rs60284537	0.82[ASN][1000 genomes]
rs61332486	0.80[ASN][1000 genomes]
rs61411293	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61466900	0.82[ASN][1000 genomes]
rs6458032	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6903743	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6906289	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6908106	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6910715	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6911716	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6936260	0.81[AFR][1000 genomes]
rs73419440	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7742226	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7745796	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7746266	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7747996	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7748312	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7759145	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759792	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7761561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7762052	0.81[AMR][1000 genomes]
rs7764130	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7773419	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7775794	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37788400-37791000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:37788600-37790400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:37788600-37790400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:37788600-37790600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:37788600-37790600	Flanking Active TSS	Liver	Liver
6	chr6:37788600-37790800	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:37788600-37791400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr6:37788600-37791400	Enhancers	Small Intestine	intestine
9	chr6:37788800-37790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:37788800-37790800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:37788800-37790800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:37788800-37790800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:37788800-37791400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:37788800-37791400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:37788800-37791400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:37788800-37791400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:37788800-37791400	Enhancers	Brain Substantia Nigra	brain
18	chr6:37788800-37791400	Enhancers	Placenta	Placenta
19	chr6:37788800-37791400	Enhancers	Fetal Stomach	stomach
20	chr6:37788800-37791600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr6:37788800-37791800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:37788800-37792000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:37788800-37792000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr6:37789000-37790400	Enhancers	Colonic Mucosa	Colon
25	chr6:37789000-37790400	Enhancers	Fetal Heart	heart
26	chr6:37789000-37790800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:37789000-37790800	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr6:37789000-37790800	Weak transcription	Aorta	Aorta
29	chr6:37789000-37791000	Enhancers	Colon Smooth Muscle	Colon
30	chr6:37789000-37791200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:37789000-37791400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr6:37789000-37791400	Enhancers	Brain Cingulate Gyrus	brain
33	chr6:37789000-37791400	Enhancers	Fetal Thymus	thymus
34	chr6:37789000-37791400	Enhancers	Ovary	ovary
35	chr6:37789000-37791400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:37789000-37791600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:37789000-37791600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:37789000-37791600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr6:37789000-37791800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:37789000-37791800	Enhancers	Left Ventricle	heart
41	chr6:37789000-37791800	Enhancers	Lung	lung
42	chr6:37789000-37791800	Enhancers	Right Atrium	heart
43	chr6:37789000-37792200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:37789000-37794400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:37789000-37796400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:37789200-37790400	Enhancers	Fetal Muscle Leg	muscle
47	chr6:37789200-37791400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:37789200-37791400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:37789200-37791400	Enhancers	Gastric	stomach
50	chr6:37789200-37791400	Enhancers	Spleen	Spleen

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