Variant report

Variant	rs2285929
Chromosome Location	chr7:27876401-27876402
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	chr7:27874082..27877005-chr7:27878628..27880591,4	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10228505	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10228576	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10245536	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10257676	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10281008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486556	0.89[EUR][1000 genomes]
rs10486562	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10951178	0.83[EUR][1000 genomes]
rs10951180	0.87[EUR][1000 genomes]
rs10951181	0.87[EUR][1000 genomes]
rs11761430	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11761467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11761905	1.00[CHB][hapmap]
rs11763610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11763861	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11765837	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11768570	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11769157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11981911	1.00[CHB][hapmap]
rs11984239	1.00[ASN][1000 genomes]
rs17150567	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17155691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17155744	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17155797	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17155802	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17155863	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17611272	0.89[EUR][1000 genomes]
rs17684444	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17692264	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17692895	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2237344	0.87[EUR][1000 genomes]
rs28432782	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28693893	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28805873	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56172733	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58979783	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61179177	1.00[ASN][1000 genomes]
rs61446104	1.00[ASN][1000 genomes]
rs62449628	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62449630	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62449641	0.83[EUR][1000 genomes]
rs62451066	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62451068	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62451069	0.87[EUR][1000 genomes]
rs62451070	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62451071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62451072	1.00[ASN][1000 genomes]
rs62451074	1.00[ASN][1000 genomes]
rs62451078	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62454809	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6979972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73075305	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73075333	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73078729	0.89[EUR][1000 genomes]
rs73078746	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73078762	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs739900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797888	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv5677	chr7:27839504-27884505	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1018550	chr7:27844038-27925645	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 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	chr7:27784800-27878400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:27806000-27882600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:27806400-27878600	Weak transcription	Right Ventricle	heart
4	chr7:27823800-27878000	Weak transcription	Spleen	Spleen
5	chr7:27824200-27876800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:27827000-27881800	Weak transcription	Small Intestine	intestine
7	chr7:27827600-27878400	Weak transcription	Fetal Kidney	kidney
8	chr7:27835200-27878200	Weak transcription	Gastric	stomach
9	chr7:27836400-27878000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:27836400-27882200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr7:27840000-27880600	Weak transcription	Hela-S3	cervix
12	chr7:27842400-27877800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:27843600-27877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr7:27847600-27885200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr7:27850200-27881400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:27854200-27882200	Weak transcription	Brain Substantia Nigra	brain
17	chr7:27856000-27882200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:27857200-27877800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:27858200-27882600	Weak transcription	Esophagus	oesophagus
20	chr7:27858400-27879600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:27858600-27880000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:27858800-27879800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr7:27858800-27880200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr7:27859800-27879400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:27860000-27881800	Weak transcription	Colonic Mucosa	Colon
26	chr7:27861400-27880800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr7:27861800-27877400	Weak transcription	Stomach Mucosa	stomach
28	chr7:27862000-27881000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:27863400-27876600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:27865400-27879000	Weak transcription	Fetal Brain Female	brain
31	chr7:27866000-27884600	Strong transcription	Primary B cells from cord blood	blood
32	chr7:27866200-27882200	Weak transcription	NHLF	lung
33	chr7:27866600-27879800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr7:27866800-27880000	Weak transcription	Aorta	Aorta
35	chr7:27867600-27877400	Weak transcription	Fetal Intestine Small	intestine
36	chr7:27868400-27878000	Weak transcription	Brain Anterior Caudate	brain
37	chr7:27868600-27876600	Weak transcription	A549	lung
38	chr7:27868600-27878400	Weak transcription	Lung	lung
39	chr7:27868600-27879600	Weak transcription	Fetal Muscle Leg	muscle
40	chr7:27869000-27879600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr7:27869000-27879600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:27869600-27882800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr7:27869800-27879600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:27870600-27891800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr7:27870800-27882200	Weak transcription	Brain Germinal Matrix	brain
46	chr7:27871400-27889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr7:27872000-27881800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:27872200-27876600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:27872200-27881600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:27872600-27879600	Weak transcription	Fetal Thymus	thymus

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