Variant report

Variant	rs6508813
Chromosome Location	chr19:39162230-39162231
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39160838..39163402-chr19:39174691..39176835,2	MCF-7	breast:
2	chr19:39156222..39158028-chr19:39160453..39162596,3	K562	blood:
3	chr19:39152656..39156169-chr19:39159383..39162487,4	K562	blood:
4	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
5	chr19:39161055..39163275-chr19:39172924..39175598,3	K562	blood:
6	chr19:39156254..39158028-chr19:39160745..39162596,2	K562	blood:
7	chr19:39161163..39163302-chr19:39198153..39200836,2	K562	blood:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1031849	0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs10421863	0.80[CHB][hapmap];0.90[CHD][hapmap];0.81[MEX][hapmap]
rs10424568	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1060186	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs11665964	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12462503	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12976749	0.81[CHB][hapmap]
rs12984247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1564203	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1985636	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2080988	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2112649	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2112651	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3786841	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3786843	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4347742	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4801861	0.89[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap]
rs4802743	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6508814	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7252630	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs749701	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs752067	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs755690	0.83[ASN][1000 genomes]
rs8099948	0.93[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8107877	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs888996	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs888997	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9304576	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs9304577	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs936524	0.94[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	nsv960837	chr19:39156364-39162333	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6508813	MEGF8	cis	cerebellum	SCAN
rs6508813	CAPN12	cis	Esophagus Muscularis	GTEx
rs6508813	CTD-2540F13.2	cis	Adipose Subcutaneous	GTEx
rs6508813	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs6508813	CAPN12	cis	Adipose Subcutaneous	GTEx
rs6508813	RPS16	cis	parietal	SCAN
rs6508813	PPP1R13L	cis	cerebellum	SCAN
rs6508813	SFRS16	cis	parietal	SCAN
rs6508813	CAPN12	cis	Heart Left Ventricle	GTEx
rs6508813	LGALS17A	cis	cerebellum	SCAN
rs6508813	CAPN12	cis	lymphoblastoid	seeQTL
rs6508813	CAPN12	cis	Muscle Skeletal	GTEx
rs6508813	CAPN12	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39152600-39164000	Enhancers	Liver	Liver
3	chr19:39154000-39162600	Enhancers	Fetal Kidney	kidney
4	chr19:39154000-39162800	Enhancers	Small Intestine	intestine
5	chr19:39154200-39162600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr19:39154600-39163000	Enhancers	Right Atrium	heart
7	chr19:39154800-39163000	Genic enhancers	Fetal Intestine Small	intestine
8	chr19:39155000-39162800	Genic enhancers	Fetal Intestine Large	intestine
9	chr19:39155200-39162800	Enhancers	Brain Angular Gyrus	brain
10	chr19:39155200-39163800	Genic enhancers	NHEK	skin
11	chr19:39155400-39162800	Enhancers	Brain Hippocampus Middle	brain
12	chr19:39155400-39162800	Enhancers	Brain Substantia Nigra	brain
13	chr19:39155800-39162400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr19:39156000-39162800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:39156400-39162800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:39156600-39164800	Enhancers	Fetal Heart	heart
17	chr19:39157800-39162600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr19:39157800-39162600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr19:39158000-39162800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr19:39158200-39162800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr19:39158200-39162800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr19:39158400-39162600	Genic enhancers	HMEC	breast
23	chr19:39158600-39162600	Enhancers	Primary B cells from peripheral blood	blood
24	chr19:39158600-39162800	Genic enhancers	Osteobl	bone
25	chr19:39158800-39162800	Enhancers	Adipose Nuclei	Adipose
26	chr19:39158800-39162800	Enhancers	Colon Smooth Muscle	Colon
27	chr19:39158800-39167600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:39159000-39165000	Weak transcription	Hela-S3	cervix
29	chr19:39159000-39166600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:39159000-39166800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:39159200-39162600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:39159400-39162800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:39159600-39162800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr19:39159600-39162800	Enhancers	Aorta	Aorta
35	chr19:39159600-39162800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr19:39159600-39169600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:39160000-39162800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:39160000-39162800	Enhancers	Brain Cingulate Gyrus	brain
39	chr19:39160000-39162800	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr19:39160200-39162800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:39160400-39162800	Enhancers	H9 Cell Line	embryonic stem cell
42	chr19:39160400-39162800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:39160400-39163000	Enhancers	Brain Anterior Caudate	brain
44	chr19:39160400-39163000	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr19:39160400-39173400	Weak transcription	Brain Germinal Matrix	brain
46	chr19:39160600-39162600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr19:39160600-39162800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr19:39160600-39162800	Enhancers	Stomach Mucosa	stomach
49	chr19:39160600-39162800	Enhancers	NH-A	brain
50	chr19:39160600-39165200	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links