Variant report

Variant	rs10431557
Chromosome Location	chr12:60092543-60092544
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:34098184..34100062-chr12:60091369..60093533,4	MCF-7	breast:
2	chr12:34097991..34100054-chr12:60091596..60093323,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10506398	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10506399	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs10877338	0.86[CHB][hapmap]
rs11173126	0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs11173133	0.83[CEU][hapmap]
rs11173159	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs12227244	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227270	0.81[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12231311	0.91[CHB][hapmap];0.87[YRI][hapmap]
rs12231693	1.00[ASW][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap]
rs12231740	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12232002	0.91[CHB][hapmap]
rs12816935	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17649424	0.91[CHB][hapmap]
rs17650311	0.91[CHB][hapmap];0.85[GIH][hapmap]
rs1795884	0.81[CHB][hapmap]
rs1795896	0.85[CHB][hapmap]
rs2706306	0.86[CHB][hapmap]
rs2706309	0.86[CHB][hapmap]
rs2706319	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs2711655	0.86[CHB][hapmap]
rs2711656	0.85[CHB][hapmap]
rs2711659	0.81[CHB][hapmap]
rs2711668	0.85[CHB][hapmap]
rs3763980	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs3847655	0.90[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61174819	0.80[EUR][1000 genomes]
rs7133415	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs7136019	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7303876	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs7976956	0.85[JPT][hapmap]
rs995342	1.00[ASW][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.97[MKK][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][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	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2829972	chr12:60079404-60111653	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv899132	chr12:60087572-60211476	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10431557	DCTN2	cis	cerebellum	SCAN
rs10431557	KIF5A	cis	cerebellum	SCAN
rs10431557	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL
rs10431557	SLC16A7	cis	lymphoblastoid	seeQTL
rs10431557	SLC16A7	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60045800-60099800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:60050800-60098600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr12:60069600-60131400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:60071600-60098600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:60072200-60098600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:60072800-60098000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr12:60085200-60098600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:60086000-60102400	Weak transcription	Primary T cells from cord blood	blood
9	chr12:60086200-60098400	Weak transcription	Primary B cells from cord blood	blood
10	chr12:60086200-60105200	Weak transcription	Aorta	Aorta
11	chr12:60086200-60106400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:60087600-60108000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:60088200-60093600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:60088400-60093400	Enhancers	NHDF-Ad	bronchial
15	chr12:60089400-60093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:60089400-60093600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:60089400-60093800	Weak transcription	HSMM	muscle
18	chr12:60089400-60126000	Weak transcription	Left Ventricle	heart
19	chr12:60089600-60093200	Weak transcription	HMEC	breast
20	chr12:60089600-60093800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:60091400-60093600	Weak transcription	Fetal Brain Male	brain
22	chr12:60091600-60093200	Weak transcription	Fetal Heart	heart
23	chr12:60092000-60093600	Enhancers	Osteobl	bone
24	chr12:60092200-60092600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:60092200-60092600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr12:60092200-60093400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:60092200-60093400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr12:60092200-60093800	Enhancers	NHEK	skin
29	chr12:60092200-60094000	Enhancers	Hela-S3	cervix
30	chr12:60092200-60094200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:60092200-60094600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:60092400-60092800	Weak transcription	NHLF	lung
33	chr12:60092400-60093000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:60092400-60093200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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