Variant report

Variant	rs9941829
Chromosome Location	chr21:17111717-17111718
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:17104089..17106756-chr21:17109896..17112248,2	MCF-7	breast:
2	chr21:17110916..17112598-chr21:17143499..17145312,2	K562	blood:
3	chr21:17077309..17079464-chr21:17110319..17112790,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10482875	0.83[CEU][hapmap]
rs10482876	1.00[CEU][hapmap]
rs11909953	0.82[YRI][hapmap]
rs11910497	0.81[AFR][1000 genomes]
rs11910884	0.81[CEU][hapmap];0.80[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs11911814	0.85[AMR][1000 genomes]
rs13347185	0.81[AFR][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]
rs1989381	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2026853	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2205585	0.85[AFR][1000 genomes]
rs2223176	0.85[AFR][1000 genomes]
rs2242676	0.91[CEU][hapmap]
rs2245574	0.82[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs2404001	0.83[CEU][hapmap]
rs2823455	0.91[CEU][hapmap]
rs2823462	0.83[CEU][hapmap]
rs2823463	0.83[CEU][hapmap]
rs2823467	0.88[AFR][1000 genomes]
rs2823469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2823470	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2823471	0.91[CEU][hapmap]
rs2823472	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2823473	0.84[AFR][1000 genomes]
rs2823476	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2823477	0.91[YRI][hapmap]
rs2823478	1.00[CEU][hapmap]
rs2823482	0.82[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2823487	0.84[YRI][hapmap]
rs2823489	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2823491	1.00[CEU][hapmap]
rs2823493	0.91[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs2823495	0.83[AFR][1000 genomes]
rs2823496	0.85[AFR][1000 genomes]
rs2823497	0.83[AFR][1000 genomes]
rs2823499	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap]
rs2823500	0.91[CEU][hapmap];0.91[YRI][hapmap]
rs2823504	0.91[CEU][hapmap]
rs28366797	0.81[AFR][1000 genomes]
rs28627435	0.88[AFR][1000 genomes]
rs28725201	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28730511	0.82[AFR][1000 genomes]
rs3787577	1.00[CEU][hapmap]
rs6517609	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6517611	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517612	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs6517613	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6517648	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6517652	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs722887	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7277807	0.83[CEU][hapmap]
rs7277813	0.85[AFR][1000 genomes]
rs7278428	0.83[CEU][hapmap]
rs7279157	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7279170	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7281511	0.91[CEU][hapmap];0.94[YRI][hapmap]
rs7283707	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8127158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8130607	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs8134327	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9974210	0.83[AFR][1000 genomes]
rs9977000	0.83[AFR][1000 genomes]
rs9981766	0.85[AFR][1000 genomes]
rs9982083	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9982479	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9983458	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9983542	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2830057	chr21:16960590-17113148	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	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:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17103200-17114400	Weak transcription	Spleen	Spleen
2	chr21:17103400-17114400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:17103800-17114400	Weak transcription	Lung	lung
4	chr21:17103800-17115000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:17104000-17114600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr21:17104000-17114600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr21:17104200-17133400	Weak transcription	Colonic Mucosa	Colon
8	chr21:17104600-17111800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr21:17104600-17113000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr21:17104600-17114600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr21:17104600-17123400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr21:17104800-17115000	Weak transcription	Fetal Muscle Leg	muscle
13	chr21:17105000-17114000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr21:17105400-17111800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr21:17105400-17112000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr21:17105400-17112200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr21:17105400-17112200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr21:17105400-17112400	Weak transcription	Brain Hippocampus Middle	brain
19	chr21:17105400-17113200	Weak transcription	NH-A	brain
20	chr21:17105400-17113600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr21:17105400-17113800	Weak transcription	HSMMtube	muscle
22	chr21:17105400-17114000	Weak transcription	HMEC	breast
23	chr21:17105400-17114400	Weak transcription	Brain Germinal Matrix	brain
24	chr21:17105400-17114800	Weak transcription	Fetal Stomach	stomach
25	chr21:17105400-17115000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr21:17105400-17115200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr21:17105400-17119400	Weak transcription	Brain Angular Gyrus	brain
28	chr21:17105400-17125200	Weak transcription	Brain Substantia Nigra	brain
29	chr21:17105800-17114600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr21:17106000-17114400	Weak transcription	Gastric	stomach
31	chr21:17106000-17114600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr21:17106200-17114800	Weak transcription	Fetal Thymus	thymus
33	chr21:17106400-17113000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr21:17106400-17114800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr21:17106400-17115200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr21:17106600-17112000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr21:17106600-17112400	Enhancers	Primary T cells from cord blood	blood
38	chr21:17106600-17113600	Weak transcription	NHEK	skin
39	chr21:17106600-17114800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr21:17106600-17116600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr21:17106800-17115200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr21:17107800-17111800	Weak transcription	Colon Smooth Muscle	Colon
43	chr21:17108000-17112000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr21:17108000-17114800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr21:17108200-17114800	Weak transcription	Fetal Intestine Small	intestine
46	chr21:17108600-17111800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr21:17108600-17112400	Weak transcription	Fetal Lung	lung
48	chr21:17108600-17112400	Weak transcription	Ovary	ovary
49	chr21:17108600-17114400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr21:17108600-17115000	Weak transcription	Placenta	Placenta

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