Variant report

Variant	rs6517609
Chromosome Location	chr21:17114496-17114497
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17101726..17104048-chr21:17113202..17115443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10482875	0.83[CEU][hapmap]
rs10482876	1.00[CEU][hapmap]
rs11910884	0.81[CEU][hapmap];0.87[CHB][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11911814	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1543299	0.91[CEU][hapmap]
rs17241416	0.91[CEU][hapmap]
rs17241423	0.89[CEU][hapmap]
rs17241430	0.91[CEU][hapmap]
rs17241444	0.91[CEU][hapmap]
rs17307120	0.83[CEU][hapmap]
rs17307176	1.00[CEU][hapmap]
rs1986788	0.80[AFR][1000 genomes]
rs1989381	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2026853	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap]
rs2205585	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2223176	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2242676	0.91[CEU][hapmap]
rs2245574	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs2404001	0.83[CEU][hapmap]
rs2823455	0.91[CEU][hapmap]
rs2823462	0.83[CEU][hapmap]
rs2823463	0.83[CEU][hapmap]
rs2823467	0.84[AFR][1000 genomes]
rs2823469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823470	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823471	0.91[CEU][hapmap]
rs2823472	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823473	0.85[AFR][1000 genomes]
rs2823476	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823477	0.87[YRI][hapmap]
rs2823478	1.00[CEU][hapmap]
rs2823482	0.88[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2823487	0.87[YRI][hapmap]
rs2823489	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2823491	1.00[CEU][hapmap]
rs2823493	0.91[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.84[ASN][1000 genomes]
rs2823495	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2823496	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2823497	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2823499	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs2823500	0.91[CEU][hapmap];0.82[CHB][hapmap];0.87[YRI][hapmap]
rs2823504	0.91[CEU][hapmap]
rs28627435	0.87[AFR][1000 genomes]
rs28725201	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28730511	0.83[AFR][1000 genomes]
rs3787577	1.00[CEU][hapmap]
rs6517611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6517612	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs6517613	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517648	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6517652	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs722887	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7277807	0.83[CEU][hapmap]
rs7277813	0.86[AFR][1000 genomes]
rs7278428	0.83[CEU][hapmap]
rs7279157	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7279170	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7281511	0.91[CEU][hapmap];0.90[YRI][hapmap]
rs7283707	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8127158	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8130607	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs8134327	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9941829	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9974210	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9977000	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9981766	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9982083	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9982479	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983458	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9983542	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases
3	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1062105	chr21:16956885-17141961	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544380	chr21:16956885-17141961	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv1815433	chr21:17106192-17167353	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17103800-17115000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:17104000-17114600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:17104000-17114600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr21:17104200-17133400	Weak transcription	Colonic Mucosa	Colon
5	chr21:17104600-17114600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr21:17104600-17123400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr21:17104800-17115000	Weak transcription	Fetal Muscle Leg	muscle
8	chr21:17105400-17114800	Weak transcription	Fetal Stomach	stomach
9	chr21:17105400-17115000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr21:17105400-17115200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr21:17105400-17119400	Weak transcription	Brain Angular Gyrus	brain
12	chr21:17105400-17125200	Weak transcription	Brain Substantia Nigra	brain
13	chr21:17105800-17114600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr21:17106000-17114600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr21:17106200-17114800	Weak transcription	Fetal Thymus	thymus
16	chr21:17106400-17114800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr21:17106400-17115200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr21:17106600-17114800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr21:17106600-17116600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr21:17106800-17115200	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr21:17108000-17114800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr21:17108200-17114800	Weak transcription	Fetal Intestine Small	intestine
23	chr21:17108600-17115000	Weak transcription	Placenta	Placenta
24	chr21:17108600-17115000	Weak transcription	Thymus	Thymus
25	chr21:17108800-17114800	Weak transcription	Dnd41	blood
26	chr21:17108800-17115200	Enhancers	HUVEC	blood vessel
27	chr21:17109400-17121000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr21:17110000-17115000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr21:17111400-17115000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr21:17111600-17117800	Enhancers	K562	blood
31	chr21:17111800-17115200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr21:17111800-17115200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr21:17112000-17114600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:17112000-17114600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr21:17112000-17114600	Weak transcription	Esophagus	oesophagus
36	chr21:17112000-17114600	Weak transcription	Left Ventricle	heart
37	chr21:17112000-17114800	Weak transcription	Fetal Intestine Large	intestine
38	chr21:17112000-17115400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr21:17112200-17115400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr21:17112400-17116200	Weak transcription	Primary T cells from cord blood	blood
41	chr21:17112600-17114600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr21:17112600-17114800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr21:17112600-17114800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr21:17112600-17118000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr21:17112800-17123400	Weak transcription	Brain Hippocampus Middle	brain
46	chr21:17113000-17114600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr21:17113000-17114600	Weak transcription	Right Ventricle	heart
48	chr21:17113000-17114800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr21:17113200-17114600	Enhancers	HSMM	muscle
50	chr21:17113200-17114800	Enhancers	Primary monocytes fromperipheralblood	blood

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