Variant report

Variant	rs6908834
Chromosome Location	chr6:87965528-87965529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:87953694..87956480-chr6:87964610..87967479,2	K562	blood:

Extended variants
information (count: 118 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1145712	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs1145713	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1145714	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1145715	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1145716	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11759727	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1188806	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1188816	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1188817	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs1188819	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1203162	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1203163	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1203164	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12194354	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12211627	0.80[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs13201289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16878497	0.84[EUR][1000 genomes]
rs1739886	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1746444	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1753152	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs181491	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1925686	0.85[EUR][1000 genomes]
rs1925689	0.81[CEU][hapmap]
rs2147917	0.81[CEU][hapmap]
rs2147918	0.81[CEU][hapmap]
rs2236048	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2257153	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs242263	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs242264	0.80[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs242265	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs242268	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs242269	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs242274	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs242275	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs242276	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs242282	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2983136	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs368267	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3734187	0.81[CEU][hapmap]
rs374792	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs377288	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs379455	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs3812130	0.81[CEU][hapmap]
rs381798	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs382956	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs384318	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3846776	0.81[CEU][hapmap]
rs385210	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3857483	0.84[CEU][hapmap]
rs3857484	0.81[CEU][hapmap]
rs3857486	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs397516	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs398140	0.98[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs3999791	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs406981	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4099964	0.81[CEU][hapmap]
rs410683	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs411606	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs413687	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs414453	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4235830	0.86[EUR][1000 genomes]
rs440296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs452315	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4707344	0.85[EUR][1000 genomes]
rs4707345	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs4707348	0.81[CEU][hapmap]
rs4707355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs540975	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs541170	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6907805	0.81[CEU][hapmap]
rs6913159	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs6913932	0.81[CEU][hapmap]
rs6921007	0.81[CEU][hapmap]
rs6921673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6926686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6927748	0.82[CEU][hapmap]
rs6932641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6933046	0.81[CEU][hapmap]
rs6934603	0.81[CEU][hapmap]
rs6938885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6939075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6940325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6940544	0.80[CEU][hapmap]
rs7752414	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7755883	0.81[CEU][hapmap]
rs7757330	0.85[EUR][1000 genomes]
rs7774603	0.81[CEU][hapmap]
rs827433	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs910564	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs912815	0.85[EUR][1000 genomes]
rs9294375	0.83[EUR][1000 genomes]
rs9294376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9344691	0.85[CEU][hapmap]
rs9344695	0.81[CEU][hapmap]
rs9353468	0.81[CEU][hapmap]
rs9359743	0.81[CEU][hapmap]
rs9362411	0.81[CEU][hapmap]
rs9362415	0.81[CEU][hapmap]
rs9444476	0.83[EUR][1000 genomes]
rs9444481	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9444486	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444488	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444490	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444491	0.93[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450623	0.84[EUR][1000 genomes]
rs9450630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9450636	0.93[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450637	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450639	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450640	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450646	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450650	0.81[CEU][hapmap]
rs9450651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450652	0.81[CEU][hapmap]
rs9450653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6908834	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs6908834	SLC35A1	cis	parietal	SCAN
rs6908834	C6orf163	cis	parietal	SCAN
rs6908834	Hs.485895	cis	multi-tissue	Pritchard
rs6908834	C6orf162	cis	parietal	SCAN
rs6908834	C6orf162	cis	cerebellum	SCAN
rs6908834	ZNF292	cis	Lymphoblastoid	GTEx
rs6908834	MDN1	cis	parietal	SCAN
rs6908834	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs6908834	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs6908834	C6orf162	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87923400-87969000	Weak transcription	Psoas Muscle	Psoas
2	chr6:87924400-87966000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:87934600-87967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:87948800-87971200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:87949600-87970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:87950200-87967600	Strong transcription	Fetal Lung	lung
7	chr6:87950200-87968200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr6:87950400-87970600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:87950400-87971400	Strong transcription	Dnd41	blood
10	chr6:87950800-87966000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:87952200-87967600	Strong transcription	Primary hematopoietic stem cells	blood
12	chr6:87953400-87968200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:87954200-87967600	Weak transcription	Stomach Mucosa	stomach
14	chr6:87954200-87970000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr6:87956800-87971800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:87957000-87969400	Weak transcription	Pancreas	Pancrea
17	chr6:87957000-87970400	Strong transcription	Placenta	Placenta
18	chr6:87957000-87971600	Weak transcription	Gastric	stomach
19	chr6:87957200-87967400	Weak transcription	Esophagus	oesophagus
20	chr6:87957200-87981000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:87958200-87968400	Strong transcription	Primary T cells from cord blood	blood
22	chr6:87959200-87968600	Weak transcription	Small Intestine	intestine
23	chr6:87959200-87969800	Weak transcription	Spleen	Spleen
24	chr6:87960200-87966000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:87960400-87968000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:87960400-87969600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:87961000-87967200	Strong transcription	Liver	Liver
28	chr6:87961000-87967600	Strong transcription	Fetal Intestine Large	intestine
29	chr6:87961000-87971600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:87961200-87965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:87961400-87968200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:87961800-87968200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:87962000-87967800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:87962200-87968400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr6:87962200-87970400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:87962200-87970600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:87962200-87970600	Strong transcription	Fetal Thymus	thymus
38	chr6:87962200-87971200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:87962400-87967800	Strong transcription	Brain Germinal Matrix	brain
40	chr6:87962400-87970400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:87962600-87966000	Strong transcription	GM12878-XiMat	blood
42	chr6:87962600-87966200	Strong transcription	Ovary	ovary
43	chr6:87962600-87967000	Strong transcription	Fetal Muscle Leg	muscle
44	chr6:87962600-87970000	Strong transcription	Primary B cells from cord blood	blood
45	chr6:87962800-87966800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:87962800-87967400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:87962800-87967400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:87962800-87967800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:87962800-87968200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr6:87962800-87968200	Strong transcription	Duodenum Mucosa	Duodenum

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