Variant report

Variant	rs6469866
Chromosome Location	chr8:120911297-120911298
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10092845	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10099088	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10102995	0.95[CEU][hapmap]
rs10955942	0.83[EUR][1000 genomes]
rs11984773	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs11984866	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs11998247	0.87[CEU][hapmap]
rs12541326	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12545586	0.84[EUR][1000 genomes]
rs12548248	0.91[CEU][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs12677306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679478	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13263147	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13265513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13265734	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13277786	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13278508	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13280041	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16893299	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1879149	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2002377	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2017310	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2056305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2139430	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2139431	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2176750	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2326432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28461628	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28546392	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28600928	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35362581	0.83[EUR][1000 genomes]
rs4073559	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4871010	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4871011	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4871786	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4871793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4871795	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56177421	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62528673	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62528677	0.83[EUR][1000 genomes]
rs62528692	0.81[EUR][1000 genomes]
rs6469860	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6469869	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6469876	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6995862	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6996081	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6999911	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7000068	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7000488	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7002423	0.81[EUR][1000 genomes]
rs7004324	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7005888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7007672	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018038	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7388491	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7461170	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7813113	0.81[YRI][hapmap]
rs7813263	0.86[CEU][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes]
rs7813430	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7823280	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7838578	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7845043	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs869340	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs869341	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9297607	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9649948	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9649949	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987135	0.83[CEU][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9987139	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9987140	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9987142	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9987165	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9987297	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv465789	chr8:120636850-120994394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv612111	chr8:120636850-120994394	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv427826	chr8:120642181-120953395	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv972194	chr8:120898451-120965081	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1018953	chr8:120910380-120954832	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6469866	DSCC1	cis	Muscle Skeletal	GTEx
rs6469866	DSCC1	cis	cerebellum	SCAN
rs6469866	DSCC1	cis	Esophagus Muscularis	GTEx
rs6469866	DSCC1	cis	Nerve Tibial	GTEx
rs6469866	DSCC1	cis	Adipose Subcutaneous	GTEx
rs6469866	VGLL2	trans	parietal	SCAN
rs6469866	DSCC1	cis	Artery Aorta	GTEx
rs6469866	DSCC1	cis	Skin Sun Exposed Lower leg	GTEx
rs6469866	DSCC1	cis	Artery Tibial	GTEx
rs6469866	DSCC1	cis	parietal	SCAN
rs6469866	DSCC1	cis	Thyroid	GTEx
rs6469866	DEPDC6	cis	cerebellum	SCAN
rs6469866	DEPTOR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120903000-120924600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr8:120905600-120911800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:120905600-120919200	Weak transcription	Fetal Kidney	kidney
4	chr8:120905800-120917400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr8:120905800-120918800	Weak transcription	Fetal Stomach	stomach
6	chr8:120906400-120915600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr8:120907600-120911600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr8:120907800-120917200	Weak transcription	Brain Substantia Nigra	brain
9	chr8:120908000-120915200	Weak transcription	Brain Anterior Caudate	brain
10	chr8:120908200-120918600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr8:120908800-120911400	Weak transcription	Brain Angular Gyrus	brain
12	chr8:120908800-120911600	Weak transcription	Liver	Liver
13	chr8:120908800-120915800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr8:120908800-120926000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:120908800-120927600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr8:120909000-120911600	Weak transcription	Brain Hippocampus Middle	brain
17	chr8:120909000-120915800	Weak transcription	Gastric	stomach
18	chr8:120909000-120915800	Weak transcription	Psoas Muscle	Psoas
19	chr8:120909000-120917400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr8:120909000-120917400	Weak transcription	Fetal Muscle Leg	muscle
21	chr8:120909000-120923400	Weak transcription	Fetal Intestine Small	intestine
22	chr8:120909000-120927200	Weak transcription	Fetal Intestine Large	intestine
23	chr8:120909000-120927600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr8:120909800-120912200	Enhancers	Colon Smooth Muscle	Colon
25	chr8:120909800-120912400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr8:120910000-120912200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr8:120910200-120911600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr8:120910600-120911600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr8:120910600-120912000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr8:120910600-120917400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr8:120910800-120927600	Weak transcription	Small Intestine	intestine
32	chr8:120911000-120912000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr8:120911000-120923000	Weak transcription	Ovary	ovary
34	chr8:120911200-120911800	Enhancers	Stomach Mucosa	stomach

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