Variant report

Variant	rs6460904
Chromosome Location	chr7:12278149-12278150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10488193	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs11980425	0.85[JPT][hapmap]
rs16877361	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17165706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17165736	0.84[EUR][1000 genomes]
rs17165737	0.84[EUR][1000 genomes]
rs17165744	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs17165746	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs17165750	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs17605315	0.96[EUR][1000 genomes]
rs60699002	0.93[EUR][1000 genomes]
rs61225336	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6978684	0.84[EUR][1000 genomes]
rs73284389	0.86[EUR][1000 genomes]
rs73301035	0.84[EUR][1000 genomes]
rs73677511	0.85[EUR][1000 genomes]
rs73677523	0.88[EUR][1000 genomes]
rs73677558	0.93[EUR][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	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12252000-12278200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:12252000-12280000	Weak transcription	Colonic Mucosa	Colon
3	chr7:12252000-12280000	Weak transcription	Right Ventricle	heart
4	chr7:12252000-12285400	Weak transcription	Spleen	Spleen
5	chr7:12252200-12279200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:12252200-12279400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:12252400-12278600	Weak transcription	NHEK	skin
8	chr7:12252400-12281600	Weak transcription	HSMMtube	muscle
9	chr7:12252400-12284000	Weak transcription	Fetal Intestine Small	intestine
10	chr7:12252600-12278200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:12252600-12279600	Weak transcription	Brain Angular Gyrus	brain
12	chr7:12252800-12279000	Weak transcription	Brain Substantia Nigra	brain
13	chr7:12254000-12279400	Strong transcription	Placenta	Placenta
14	chr7:12255200-12279000	Strong transcription	Liver	Liver
15	chr7:12256400-12279400	Weak transcription	Psoas Muscle	Psoas
16	chr7:12256600-12279600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:12257200-12278400	Weak transcription	Fetal Brain Female	brain
18	chr7:12259000-12278800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:12259800-12283600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:12260400-12279400	Weak transcription	NHDF-Ad	bronchial
21	chr7:12263200-12279400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr7:12264200-12279800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr7:12264200-12280000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr7:12264200-12280000	Weak transcription	Ovary	ovary
25	chr7:12264400-12279400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:12264600-12279600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr7:12264600-12279600	Weak transcription	Fetal Thymus	thymus
28	chr7:12264600-12279800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:12266400-12279400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:12266400-12279600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr7:12266400-12279800	Weak transcription	Small Intestine	intestine
32	chr7:12267000-12279000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr7:12270000-12284400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:12270200-12279000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr7:12270200-12279600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr7:12271600-12278600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:12271800-12279600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr7:12271800-12280000	Weak transcription	Osteobl	bone
39	chr7:12271800-12289000	Weak transcription	HSMM	muscle
40	chr7:12272000-12278600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr7:12272000-12278800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:12272000-12279200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr7:12272200-12279600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr7:12272400-12280000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:12274200-12278200	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:12274600-12278800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr7:12274600-12279200	Weak transcription	Primary B cells from cord blood	blood
48	chr7:12274800-12280000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr7:12275600-12278400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr7:12277000-12278200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links