Variant report

Variant	rs871183
Chromosome Location	chr6:38288168-38288169
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	chr6:38275306..38278894-chr6:38287022..38290918,3	MCF-7	breast:
2	chr6:38286667..38288698-chr6:38291233..38294146,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1033480	0.92[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10947725	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10947726	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10947728	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947729	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11759824	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1205108	1.00[CHB][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12191714	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12201631	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12202804	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12206324	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12206905	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12208912	0.85[EUR][1000 genomes]
rs12212983	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12215330	0.81[CEU][hapmap]
rs12215850	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1883610	0.86[JPT][hapmap]
rs1931758	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1983605	1.00[JPT][hapmap]
rs2179532	0.81[EUR][1000 genomes]
rs2179533	0.80[EUR][1000 genomes]
rs228179	0.92[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs228180	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs228186	0.92[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs228188	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs28445226	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4236058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711542	1.00[JPT][hapmap]
rs4711546	1.00[JPT][hapmap]
rs4714152	1.00[JPT][hapmap]
rs4714157	1.00[JPT][hapmap]
rs4714165	0.88[JPT][hapmap]
rs6899746	1.00[JPT][hapmap]
rs6901086	1.00[JPT][hapmap]
rs6904723	1.00[JPT][hapmap]
rs6933268	1.00[JPT][hapmap]
rs6933758	1.00[JPT][hapmap]
rs6940319	1.00[JPT][hapmap]
rs742515	1.00[JPT][hapmap]
rs7748599	1.00[JPT][hapmap]
rs7749685	1.00[JPT][hapmap]
rs7759629	1.00[JPT][hapmap]
rs7763775	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7766214	1.00[JPT][hapmap]
rs7770868	1.00[JPT][hapmap]
rs9349073	1.00[JPT][hapmap]
rs9357272	1.00[JPT][hapmap]
rs9380743	1.00[JPT][hapmap]
rs9394495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9470885	1.00[JPT][hapmap]
rs9470888	1.00[JPT][hapmap]
rs9470891	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs871183	TMEM217	cis	parietal	SCAN
rs871183	GLO1	cis	parietal	SCAN
rs871183	C6orf64	cis	cerebellum	SCAN
rs871183	TRERF1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38274400-38288600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:38275400-38301200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:38278000-38310600	Weak transcription	Gastric	stomach
4	chr6:38278200-38295000	Weak transcription	Lung	lung
5	chr6:38278400-38305400	Weak transcription	Pancreas	Pancrea
6	chr6:38282600-38301400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:38283000-38304000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:38284200-38296000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:38284800-38301200	Weak transcription	Fetal Intestine Small	intestine
10	chr6:38285000-38327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:38285200-38288200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:38286800-38290000	Enhancers	Fetal Muscle Leg	muscle
13	chr6:38286800-38291000	Weak transcription	Psoas Muscle	Psoas
14	chr6:38286800-38295400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:38287200-38289400	Enhancers	Brain Anterior Caudate	brain
16	chr6:38287400-38288400	Weak transcription	Fetal Stomach	stomach
17	chr6:38287400-38289200	Enhancers	Brain Substantia Nigra	brain
18	chr6:38287400-38289400	Enhancers	Brain Germinal Matrix	brain
19	chr6:38287400-38289600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:38287400-38301200	Weak transcription	Primary B cells from cord blood	blood
21	chr6:38287600-38288200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:38287600-38289400	Flanking Active TSS	GM12878-XiMat	blood
23	chr6:38287600-38290000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:38287600-38301200	Weak transcription	Primary T cells from cord blood	blood
25	chr6:38287800-38288400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:38287800-38288400	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr6:38287800-38289400	Enhancers	Fetal Brain Male	brain
28	chr6:38287800-38290000	Enhancers	Brain Hippocampus Middle	brain
29	chr6:38288000-38288200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:38288000-38289800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:38288000-38290000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:38288000-38290800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:38288000-38290800	Weak transcription	HSMMtube	muscle
34	chr6:38288000-38291000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:38288000-38291000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:38288000-38291600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr6:38288000-38292800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:38288000-38305600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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