Variant report

Variant	rs6583817
Chromosome Location	chr10:94247247-94247248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10786047	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882066	0.82[ASN][1000 genomes]
rs10882069	0.80[ASN][1000 genomes]
rs10882086	0.89[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap]
rs10882088	0.89[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap]
rs11186999	0.82[ASN][1000 genomes]
rs11187000	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11187003	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11187004	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11187013	0.81[ASN][1000 genomes]
rs11187016	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187035	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11187037	0.82[ASN][1000 genomes]
rs11187060	0.80[JPT][hapmap]
rs11187108	0.89[CHB][hapmap];0.86[GIH][hapmap]
rs11187115	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs11595187	0.89[CHB][hapmap]
rs11814555	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12415807	0.82[ASN][1000 genomes]
rs12416180	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs17107734	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1832197	0.80[JPT][hapmap]
rs1999763	0.89[CHB][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap]
rs1999764	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2275219	0.89[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap]
rs2297743	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2421940	0.96[GIH][hapmap];0.84[JPT][hapmap]
rs3758503	0.89[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap]
rs3758505	0.89[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap]
rs3781240	0.86[EUR][1000 genomes]
rs4646954	0.93[GIH][hapmap];0.84[JPT][hapmap]
rs4933231	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4933232	0.82[ASN][1000 genomes]
rs4933725	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4933726	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4933731	0.88[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap]
rs6583815	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6583820	0.88[ASW][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs7068618	0.88[ASW][hapmap];0.89[CHB][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7075073	0.82[ASN][1000 genomes]
rs7075851	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7079099	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs7087153	0.87[AFR][1000 genomes]
rs7091270	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7093437	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7097800	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898862	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7900584	0.89[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap]
rs7910605	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7910977	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7911558	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv551924	chr10:94212742-94290484	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv551925	chr10:94224165-94288429	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1802816	chr10:94232247-94294291	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv1792868	chr10:94232247-94409749	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6583817	SLC16A12	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94208400-94276800	Weak transcription	Stomach Mucosa	stomach
2	chr10:94210600-94250000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:94211400-94253200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:94212800-94270400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:94217400-94251800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:94217600-94270200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr10:94218200-94251800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:94222800-94250800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:94223200-94252600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:94225400-94248800	Weak transcription	Brain Germinal Matrix	brain
11	chr10:94225600-94248400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr10:94225600-94252600	Weak transcription	Fetal Kidney	kidney
13	chr10:94227400-94251200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:94230000-94276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr10:94230200-94247800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:94230400-94276400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:94230600-94249000	Weak transcription	NHLF	lung
18	chr10:94230600-94249400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr10:94232800-94251200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr10:94233200-94251000	Strong transcription	Liver	Liver
21	chr10:94233200-94254000	Strong transcription	Adipose Nuclei	Adipose
22	chr10:94233600-94250600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:94233800-94251200	Strong transcription	Left Ventricle	heart
24	chr10:94236400-94253000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr10:94236600-94251000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:94236800-94248800	Weak transcription	Colon Smooth Muscle	Colon
27	chr10:94237200-94251200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr10:94237400-94250400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:94237800-94250400	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr10:94237800-94251000	Strong transcription	Brain Anterior Caudate	brain
31	chr10:94238000-94254000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr10:94239600-94248800	Weak transcription	NH-A	brain
33	chr10:94239600-94252400	Weak transcription	HMEC	breast
34	chr10:94239600-94280400	Weak transcription	Fetal Brain Male	brain
35	chr10:94239800-94248000	Weak transcription	HSMMtube	muscle
36	chr10:94240200-94265400	Weak transcription	Fetal Heart	heart
37	chr10:94241000-94250600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:94241200-94247800	Weak transcription	NHEK	skin
39	chr10:94242400-94254200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr10:94242600-94247400	Strong transcription	Osteobl	bone
41	chr10:94242800-94250400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:94242800-94250600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr10:94242800-94250600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr10:94242800-94250600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr10:94242800-94253000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr10:94243000-94248600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr10:94243000-94249000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:94243000-94250200	Strong transcription	Brain Hippocampus Middle	brain
49	chr10:94243000-94250600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr10:94243000-94250600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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