Variant report

Variant	rs6958427
Chromosome Location	chr7:21952954-21952955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1406705	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4540316	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6461618	1.00[YRI][hapmap]
rs6461624	0.90[YRI][hapmap]
rs6978729	0.82[ASN][1000 genomes]
rs7811959	1.00[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	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv2086235	chr7:21952954-21952955	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6958427	RAPGEF5	cis	lymphoblastoid	seeQTL
rs6958427	TM7SF3	trans	brain	seeQTL
rs6958427	PIP5K1B	trans	brain	seeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21933000-21963200	Weak transcription	A549	lung
2	chr7:21936600-21956400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr7:21936600-21956600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:21937000-21956400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:21937200-21956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:21937400-21956000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:21937600-21956200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:21937600-21956400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:21937800-21954000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:21937800-21956000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr7:21937800-21956200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:21938000-21955000	Weak transcription	Stomach Mucosa	stomach
13	chr7:21938000-21956200	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr7:21938600-21984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr7:21938800-21953200	Strong transcription	Fetal Thymus	thymus
16	chr7:21938800-21956600	Strong transcription	Primary T cells from cord blood	blood
17	chr7:21942000-21955400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:21942400-21957200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:21943000-21955000	Weak transcription	Fetal Kidney	kidney
20	chr7:21944000-21954800	Weak transcription	NH-A	brain
21	chr7:21944000-21957400	Weak transcription	Colonic Mucosa	Colon
22	chr7:21944200-21953200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:21944200-21956200	Weak transcription	Spleen	Spleen
24	chr7:21944400-21956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:21946000-21956200	Weak transcription	Brain Substantia Nigra	brain
26	chr7:21946000-21956400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:21946200-21954600	Weak transcription	Esophagus	oesophagus
28	chr7:21946200-21955600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr7:21946200-21957600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr7:21946200-21963400	Weak transcription	Brain Hippocampus Middle	brain
31	chr7:21946400-21953800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:21946600-21953400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr7:21947800-21953000	Weak transcription	NHEK	skin
34	chr7:21947800-21956000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr7:21947800-21958000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:21948000-21953600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:21948000-21953800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr7:21948200-21956400	Weak transcription	Fetal Intestine Large	intestine
39	chr7:21948400-21953400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:21948400-21956400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr7:21948400-21960400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:21948600-21953200	Weak transcription	Lung	lung
43	chr7:21948600-21953400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:21948800-21953400	Weak transcription	Brain Anterior Caudate	brain
45	chr7:21948800-21981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr7:21949000-21953000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr7:21949200-21953200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:21949200-21953200	Weak transcription	HMEC	breast
49	chr7:21949200-21953200	Weak transcription	HUVEC	blood vessel
50	chr7:21949400-21953200	Enhancers	Fetal Heart	heart

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