Variant report

Variant	rs12173920
Chromosome Location	chr6:34887316-34887317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34852396..34857039-chr6:34885312..34888900,5	MCF-7	breast:
2	chr6:34879811..34884262-chr6:34884635..34888970,5	K562	blood:
3	chr6:34887307..34889419-chr6:34914664..34917494,2	MCF-7	breast:
4	chr6:34878922..34882866-chr6:34883896..34887915,4	MCF-7	breast:
5	chr6:34887280..34889976-chr6:34890282..34893090,2	K562	blood:
6	chr6:34758555..34760714-chr6:34886216..34888583,2	K562	blood:
7	chr6:34880699..34884444-chr6:34885944..34888970,5	K562	blood:

Variant related genes	Relation type
ENSG00000064995	Chromatin interaction
ENSG00000065060	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11970238	0.82[ASN][1000 genomes]
rs12175621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12176092	0.89[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16894102	0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs16894945	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16894995	0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs16895362	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16895467	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16896235	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2273007	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2764199	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs3734260	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3734263	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756857	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3777751	0.81[ASN][1000 genomes]
rs3798349	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs3800439	0.82[ASN][1000 genomes]
rs3800442	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3800447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3800449	0.89[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3807051	0.85[ASN][1000 genomes]
rs4646923	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56825685	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57338415	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57608318	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57637041	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58654146	0.81[ASN][1000 genomes]
rs58764768	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58817410	0.81[ASN][1000 genomes]
rs58833137	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59851773	0.81[ASN][1000 genomes]
rs60439875	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs60509690	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60815469	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6939345	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs73403805	0.82[ASN][1000 genomes]
rs73419615	0.81[ASN][1000 genomes]
rs73419643	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73419650	0.83[ASN][1000 genomes]
rs73419656	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73419658	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73419660	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73419689	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73421513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73421527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73421528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73421536	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73421541	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs847849	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348952	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9348954	0.89[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9348955	0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348956	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9348957	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs9357186	0.89[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357189	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357191	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9366871	0.93[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9366873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9368840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368842	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368844	0.81[ASN][1000 genomes]
rs9380471	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380472	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380475	0.84[ASN][1000 genomes]
rs9380478	0.82[ASN][1000 genomes]
rs9394253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9394257	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394259	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9394261	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394262	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394264	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9394265	0.94[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs9394267	0.94[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1025374	chr6:34723723-34887316	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1015792	chr6:34741917-34887316	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv1021733	chr6:34751052-34887316	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv1026121	chr6:34786887-34961360	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv885797	chr6:34791027-34980601	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
10	nsv1033135	chr6:34802652-34957093	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
11	nsv508402	chr6:34840961-34951288	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12173920	C6orf107	cis	multi-tissue	Pritchard
rs12173920	CTSL1	cis	Liver	GTEx
rs12173920	STEAP4	cis	Liver	GTEx
rs12173920	CTSL	trans	multi-tissue	Pritchard
rs12173920	STEAP4	trans	multi-tissue	Pritchard
rs12173920	UHRF1BP1	cis	Liver	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34859200-34890800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:34869600-34890000	Weak transcription	Hela-S3	cervix
3	chr6:34872400-34907200	Weak transcription	Small Intestine	intestine
4	chr6:34874400-34893200	Weak transcription	Fetal Intestine Large	intestine
5	chr6:34874800-34896000	Weak transcription	Brain Anterior Caudate	brain
6	chr6:34877000-34890000	Weak transcription	K562	blood
7	chr6:34877800-34892200	Weak transcription	Brain Angular Gyrus	brain
8	chr6:34877800-34921000	Weak transcription	Pancreas	Pancrea
9	chr6:34878000-34891400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:34878000-34896400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:34879600-34892200	Weak transcription	Fetal Intestine Small	intestine
12	chr6:34879600-34892200	Weak transcription	Fetal Kidney	kidney
13	chr6:34879600-34893200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:34879600-34896800	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:34879800-34891800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:34879800-34893000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:34880000-34888800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:34880800-34893400	Weak transcription	Fetal Thymus	thymus
19	chr6:34881000-34889200	Weak transcription	Primary B cells from cord blood	blood
20	chr6:34881000-34898000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:34881200-34890200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:34881200-34893000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:34881200-34928200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:34881400-34887600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:34881400-34890000	Weak transcription	HMEC	breast
26	chr6:34881400-34896600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:34881400-34902800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:34881600-34890600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:34881600-34891800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:34883800-34888000	Enhancers	Adipose Nuclei	Adipose
31	chr6:34884400-34887400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:34884800-34887400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:34884800-34888800	Enhancers	Right Ventricle	heart
34	chr6:34885200-34894400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:34885600-34887400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:34885600-34890200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:34885600-34894400	Weak transcription	Placenta	Placenta
38	chr6:34885800-34892600	Weak transcription	Liver	Liver
39	chr6:34885800-34895400	Weak transcription	Gastric	stomach
40	chr6:34885800-34902200	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:34885800-34902400	Weak transcription	Fetal Stomach	stomach
42	chr6:34886000-34887400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:34886000-34887800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:34886000-34891200	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:34886000-34891400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:34886000-34891600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:34886200-34892400	Weak transcription	HepG2	liver
48	chr6:34886400-34887600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:34886400-34891800	Weak transcription	Fetal Lung	lung
50	chr6:34886400-34893000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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