Variant report

Variant	rs10875685
Chromosome Location	chr12:48132159-48132160
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48119660..48121319-chr12:48130361..48132354,2	MCF-7	breast:
2	chr12:48128880..48137705-chr12:48169546..48175532,12	K562	blood:
3	chr12:48129185..48133424-chr12:48134380..48137725,4	MCF-7	breast:
4	chr12:48125574..48127133-chr12:48129980..48132497,2	MCF-7	breast:
5	chr12:48130227..48133339-chr12:48139533..48144417,5	K562	blood:
6	chr12:48130735..48132314-chr12:48133674..48136092,2	MCF-7	breast:
7	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000211584	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10783212	0.82[ASN][1000 genomes]
rs10875677	0.81[ASN][1000 genomes]
rs10875682	0.80[ASN][1000 genomes]
rs10875686	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875687	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875688	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168191	0.80[ASN][1000 genomes]
rs11168192	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs11168193	0.80[ASN][1000 genomes]
rs11168199	0.89[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11168200	0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11168203	0.82[ASN][1000 genomes]
rs11168208	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168214	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168215	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12366410	0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs12370643	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs2072117	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240079	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240080	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283346	0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764013	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61917595	0.82[ASN][1000 genomes]
rs61917616	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61917617	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580634	0.84[ASN][1000 genomes]
rs7136561	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7308119	0.86[LWK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs7311663	0.89[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7484827	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969186	0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7976748	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7977613	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers 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 lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription 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	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10875685	TMEM117	cis	cerebellum	SCAN
rs10875685	SENP1	cis	parietal	SCAN
rs10875685	ENDOU	cis	Thyroid	GTEx
rs10875685	HDAC7	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48114000-48134400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:48114200-48132600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:48115600-48133600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:48115600-48134200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:48115600-48135000	Weak transcription	Primary T cells from cord blood	blood
6	chr12:48116200-48134000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:48125400-48132200	Enhancers	Fetal Muscle Leg	muscle
8	chr12:48125600-48132200	Enhancers	Brain Substantia Nigra	brain
9	chr12:48126800-48132400	Enhancers	Brain Angular Gyrus	brain
10	chr12:48126800-48133400	Enhancers	Ovary	ovary
11	chr12:48127000-48134000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:48127600-48135800	Enhancers	Fetal Muscle Trunk	muscle
13	chr12:48128000-48132600	Enhancers	Brain Anterior Caudate	brain
14	chr12:48128200-48132600	Enhancers	Fetal Heart	heart
15	chr12:48128200-48132600	Enhancers	Left Ventricle	heart
16	chr12:48128200-48135600	Enhancers	Right Atrium	heart
17	chr12:48128400-48135000	Weak transcription	NHEK	skin
18	chr12:48128600-48132200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:48128600-48132200	Enhancers	Pancreas	Pancrea
20	chr12:48128800-48132200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr12:48128800-48132400	Enhancers	Duodenum Mucosa	Duodenum
22	chr12:48128800-48132600	Enhancers	NHDF-Ad	bronchial
23	chr12:48129000-48132200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:48129200-48134000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:48129200-48134600	Weak transcription	Fetal Brain Female	brain
27	chr12:48129200-48137600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:48129400-48134000	Weak transcription	Fetal Brain Male	brain
29	chr12:48129400-48134200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:48129400-48138600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:48129600-48132200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:48129600-48133000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:48129800-48132400	Enhancers	Brain Cingulate Gyrus	brain
35	chr12:48129800-48137600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:48130000-48132400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr12:48130000-48132400	Genic enhancers	Fetal Stomach	stomach
38	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
39	chr12:48130200-48132200	Enhancers	Adipose Nuclei	Adipose
40	chr12:48130200-48134800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:48130400-48134600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:48130400-48137600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:48130600-48133600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:48130600-48138800	Weak transcription	Fetal Intestine Large	intestine
45	chr12:48130800-48132200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:48130800-48132400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:48130800-48132800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:48130800-48133600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr12:48130800-48134600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:48131000-48132400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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