Variant report

Variant	rs4616340
Chromosome Location	chr17:17861360-17861361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17850477..17852579-chr17:17859985..17861970,2	MCF-7	breast:
2	chr17:17855039..17859683-chr17:17860221..17864104,5	MCF-7	breast:
3	chr17:17861024..17862929-chr17:17866767..17869059,2	MCF-7	breast:
4	chr17:17861263..17864365-chr17:17940983..17943092,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171953	Chromatin interaction
ENSG00000141034	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10048206	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11078400	0.80[EUR][1000 genomes]
rs11078403	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11078404	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11078405	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11078406	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078407	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078408	0.84[EUR][1000 genomes]
rs11650649	0.90[EUR][1000 genomes]
rs11650890	0.90[EUR][1000 genomes]
rs11656840	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11657773	0.84[EUR][1000 genomes]
rs11657845	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11869536	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11870660	0.83[EUR][1000 genomes]
rs11871899	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12452219	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12452254	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12600546	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12603148	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2350977	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28428991	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4077198	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4077828	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4244602	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4257260	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299203	0.83[EUR][1000 genomes]
rs4321247	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4341796	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4343339	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4413022	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4414547	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4470201	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4471742	0.84[EUR][1000 genomes]
rs4534911	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4553680	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4925123	0.90[EUR][1000 genomes]
rs4925125	0.91[EUR][1000 genomes]
rs4925126	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4925129	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925130	0.94[EUR][1000 genomes]
rs5002487	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57728924	0.83[EUR][1000 genomes]
rs62064156	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62064158	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62072049	0.84[EUR][1000 genomes]
rs6502619	0.90[EUR][1000 genomes]
rs6502622	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6502624	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6502625	0.88[EUR][1000 genomes]
rs6502626	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502627	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502629	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66531105	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67253360	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7207043	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7207395	0.96[EUR][1000 genomes]
rs7208190	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7213225	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7214002	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214536	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219320	0.82[EUR][1000 genomes]
rs7222480	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7224815	0.82[EUR][1000 genomes]
rs7503334	0.90[EUR][1000 genomes]
rs8065416	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065563	0.90[EUR][1000 genomes]
rs8065970	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066982	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068175	0.83[EUR][1000 genomes]
rs8068820	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8070128	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8070722	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8070748	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073001	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8075965	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8076747	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077338	0.83[EUR][1000 genomes]
rs8077530	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8078105	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8078138	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8078583	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8080061	0.81[EUR][1000 genomes]
rs8080823	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs950966	0.90[EUR][1000 genomes]
rs9635697	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9635698	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9890341	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9904163	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9905284	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9907287	0.81[EUR][1000 genomes]
rs9908017	0.81[EUR][1000 genomes]
rs9908832	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9912895	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9913724	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9914127	0.84[EUR][1000 genomes]

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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17844800-17861400	Weak transcription	Liver	Liver
2	chr17:17847200-17861400	Weak transcription	Fetal Kidney	kidney
3	chr17:17847400-17861600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr17:17847400-17864000	Weak transcription	Aorta	Aorta
5	chr17:17848400-17862200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr17:17848600-17861400	Weak transcription	Brain Substantia Nigra	brain
7	chr17:17848600-17861600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr17:17848800-17863000	Weak transcription	Fetal Brain Female	brain
9	chr17:17849000-17861600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:17852800-17862000	Weak transcription	Pancreas	Pancrea
11	chr17:17853000-17861600	Weak transcription	Brain Angular Gyrus	brain
12	chr17:17855200-17862000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:17855400-17861400	Weak transcription	Brain Anterior Caudate	brain
14	chr17:17855600-17861400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr17:17855600-17861400	Weak transcription	Fetal Lung	lung
16	chr17:17856200-17862400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr17:17856400-17861400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr17:17857000-17861800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr17:17857000-17861800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr17:17857200-17862000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr17:17857400-17862000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr17:17857600-17863000	Weak transcription	Ovary	ovary
23	chr17:17858200-17861600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr17:17858400-17862800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr17:17859000-17863000	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr17:17859200-17861400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr17:17859200-17861600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr17:17859400-17862800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr17:17859600-17861400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr17:17859600-17863800	Enhancers	Right Ventricle	heart
31	chr17:17859800-17861600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr17:17859800-17861600	Enhancers	NHDF-Ad	bronchial
33	chr17:17859800-17862400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr17:17859800-17862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:17859800-17862600	Enhancers	Lung	lung
36	chr17:17859800-17862600	Enhancers	Stomach Mucosa	stomach
37	chr17:17859800-17862600	Enhancers	Spleen	Spleen
38	chr17:17859800-17863000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr17:17859800-17863000	Enhancers	Right Atrium	heart
40	chr17:17859800-17863600	Enhancers	HMEC	breast
41	chr17:17859800-17864000	Enhancers	Left Ventricle	heart
42	chr17:17860000-17861800	Weak transcription	Fetal Stomach	stomach
43	chr17:17860000-17862000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:17860200-17861400	Enhancers	NHEK	skin
45	chr17:17860200-17861600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr17:17860200-17862000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr17:17860200-17862400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:17860200-17862600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr17:17860200-17862800	Enhancers	Primary T cells from cord blood	blood
50	chr17:17860200-17862800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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