Variant report

Variant	rs6946420
Chromosome Location	chr7:138209685-138209686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:138209195..138211735-chr7:138245939..138248428,2	K562	blood:
2	chr7:138208149..138212186-chr7:138212617..138217057,4	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10236035	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10271000	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10272245	0.92[CEU][hapmap]
rs11761566	0.92[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11976228	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11981542	1.00[CHB][hapmap]
rs12707387	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12707388	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2353353	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs3213902	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4535683	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467774	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6467777	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6467779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6467781	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6947224	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6948094	0.82[LWK][hapmap]
rs6962037	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6970145	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7782453	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7794786	0.82[EUR][1000 genomes]
rs7799818	0.84[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap]
rs7803989	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7811152	0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831153	chr7:138078179-138265648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6946420	ZC3HAV1L	cis	cerebellum	SCAN
rs6946420	JHDM1D	cis	cerebellum	SCAN
rs6946420	SSBP1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138177000-138212600	Weak transcription	Pancreas	Pancrea
2	chr7:138178600-138212200	Weak transcription	NHLF	lung
3	chr7:138186600-138210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:138188400-138209800	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr7:138188800-138210400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:138188800-138210600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:138190200-138212200	Weak transcription	HMEC	breast
8	chr7:138192000-138212200	Weak transcription	Stomach Mucosa	stomach
9	chr7:138194000-138212000	Weak transcription	NHDF-Ad	bronchial
10	chr7:138195200-138212200	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:138197000-138216000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:138197400-138210600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:138197400-138212600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:138197600-138210400	Weak transcription	A549	lung
15	chr7:138197600-138211800	Weak transcription	Fetal Brain Male	brain
16	chr7:138197600-138212600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:138198000-138210800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:138198000-138212200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr7:138199200-138212200	Weak transcription	Brain Anterior Caudate	brain
20	chr7:138199400-138210400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr7:138199400-138212400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:138200000-138210400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr7:138200200-138210400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:138200200-138210600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:138201200-138212200	Strong transcription	Liver	Liver
26	chr7:138201800-138210600	Weak transcription	Esophagus	oesophagus
27	chr7:138202200-138212200	Weak transcription	Small Intestine	intestine
28	chr7:138203600-138210200	Strong transcription	Fetal Lung	lung
29	chr7:138204200-138211600	Weak transcription	Fetal Heart	heart
30	chr7:138204400-138210000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr7:138204400-138210600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:138204400-138210600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:138204400-138210600	Weak transcription	Brain Angular Gyrus	brain
34	chr7:138204400-138212000	Weak transcription	Brain Substantia Nigra	brain
35	chr7:138204400-138212200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:138204400-138212200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:138204400-138212400	Weak transcription	NHEK	skin
38	chr7:138204600-138216200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:138204800-138210600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr7:138204800-138210600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr7:138204800-138210600	Weak transcription	HSMM	muscle
42	chr7:138204800-138212200	Weak transcription	HUVEC	blood vessel
43	chr7:138204800-138212600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:138205000-138210400	Weak transcription	Fetal Brain Female	brain
45	chr7:138205000-138210600	Weak transcription	Lung	lung
46	chr7:138205000-138210600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr7:138205000-138212200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:138205000-138212200	Weak transcription	Psoas Muscle	Psoas
49	chr7:138205000-138212400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:138205000-138212400	Weak transcription	Gastric	stomach

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