Variant report

Variant	rs690872
Chromosome Location	chr7:129105535-129105536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129091760..129094505-chr7:129102793..129105599,2	K562	blood:
2	chr7:129070406..129072792-chr7:129104561..129108089,3	MCF-7	breast:
3	chr7:129082084..129084062-chr7:129103649..129105975,2	K562	blood:
4	chr7:129071464..129074294-chr7:129104597..129106505,2	K562	blood:
5	chr7:129102197..129105819-chr7:129107947..129111490,3	K562	blood:

Variant related genes	Relation type
ENSG00000128578	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10224011	0.82[CHB][hapmap]
rs11768964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs11771549	0.85[CHB][hapmap]
rs1272593	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402951	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs2598183	0.85[CHB][hapmap]
rs55832716	0.85[EUR][1000 genomes]
rs581829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586978	0.81[AFR][1000 genomes]
rs587499	0.85[CHB][hapmap];0.85[YRI][hapmap]
rs610591	0.82[CHB][hapmap]
rs613068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs613169	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs632505	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs655239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs656981	0.92[EUR][1000 genomes]
rs657664	1.00[CHB][hapmap]
rs666499	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs690903	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs691303	0.85[CHB][hapmap]
rs691325	0.85[CHB][hapmap];0.82[YRI][hapmap]
rs691476	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs692132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs692248	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692507	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs692686	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692695	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969620	0.82[CHB][hapmap]
rs712692	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712693	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7787531	0.81[CEU][hapmap];0.82[CHB][hapmap]

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	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv831128	chr7:129063040-129240800	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129075200-129108400	Weak transcription	Gastric	stomach
2	chr7:129075400-129105800	Weak transcription	Ovary	ovary
3	chr7:129076000-129110000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:129077400-129109400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:129079600-129107200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:129079800-129106400	Weak transcription	NHDF-Ad	bronchial
7	chr7:129080000-129128000	Weak transcription	HUVEC	blood vessel
8	chr7:129082600-129108400	Weak transcription	Thymus	Thymus
9	chr7:129083800-129112800	Strong transcription	K562	blood
10	chr7:129089200-129106600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:129089400-129108400	Weak transcription	Fetal Lung	lung
12	chr7:129089400-129110000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:129089600-129106400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:129089600-129110200	Weak transcription	Brain Substantia Nigra	brain
15	chr7:129091600-129109200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:129091800-129108800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:129092600-129109200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:129092800-129106800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:129093200-129109400	Weak transcription	Fetal Thymus	thymus
20	chr7:129093400-129105600	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr7:129093400-129134800	Weak transcription	Right Atrium	heart
22	chr7:129094800-129107400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:129094800-129107800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:129094800-129108200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:129095000-129105600	Strong transcription	HMEC	breast
26	chr7:129095000-129105800	Strong transcription	NHEK	skin
27	chr7:129095000-129107800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:129095200-129111800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:129095400-129109800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:129095400-129115000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:129096400-129109200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:129096800-129108400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:129096800-129110200	Weak transcription	Small Intestine	intestine
34	chr7:129096800-129112000	Weak transcription	GM12878-XiMat	blood
35	chr7:129097200-129110200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:129097600-129128600	Weak transcription	NH-A	brain
37	chr7:129099000-129107800	Weak transcription	Brain Germinal Matrix	brain
38	chr7:129100400-129105800	Weak transcription	HSMMtube	muscle
39	chr7:129100400-129113000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:129100600-129106600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:129100800-129106400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:129100800-129107600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:129101000-129109400	Weak transcription	Brain Angular Gyrus	brain
44	chr7:129101400-129109600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:129101600-129128600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr7:129102200-129124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:129102400-129108200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr7:129102400-129120400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:129103000-129105600	Weak transcription	HSMM	muscle
50	chr7:129103000-129106000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links