Variant report

Variant	rs10846580
Chromosome Location	chr12:124415453-124415454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr12:124415303-124415466	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
DNAH10	TF binding region
ENSG00000270028	TF binding region

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1054852	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs10846577	0.92[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.87[MKK][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs10846578	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10846579	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057393	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11057394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11057397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057399	0.98[EUR][1000 genomes]
rs11057400	0.90[EUR][1000 genomes]
rs11057401	0.92[CEU][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap];0.90[EUR][1000 genomes]
rs11057407	0.88[EUR][1000 genomes]
rs11057408	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs11057409	1.00[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs11057412	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11057413	0.96[EUR][1000 genomes]
rs11831913	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11833002	0.99[EUR][1000 genomes]
rs11835839	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11837287	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1187415	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12296259	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12298484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12301673	0.97[EUR][1000 genomes]
rs12303671	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12303933	0.95[EUR][1000 genomes]
rs12310367	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12311114	0.92[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs12311848	0.95[EUR][1000 genomes]
rs12316080	0.97[EUR][1000 genomes]
rs12317176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12322694	0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12809125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12809473	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12823740	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs12824567	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs12827409	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12829951	0.98[EUR][1000 genomes]
rs12833624	0.96[EUR][1000 genomes]
rs1882491	0.87[EUR][1000 genomes]
rs2130382	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2178663	0.92[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs3186071	0.90[EUR][1000 genomes]
rs34114498	0.97[EUR][1000 genomes]
rs34180676	0.87[EUR][1000 genomes]
rs34854841	0.89[EUR][1000 genomes]
rs34878139	0.99[EUR][1000 genomes]
rs35099862	0.96[EUR][1000 genomes]
rs35825716	0.90[EUR][1000 genomes]
rs3789967	0.97[EUR][1000 genomes]
rs3802999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4405410	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4575361	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4765127	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs4765148	0.92[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs4765219	1.00[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs4765305	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4765335	0.90[EUR][1000 genomes]
rs4765528	0.92[CEU][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs4765541	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4765562	0.97[EUR][1000 genomes]
rs4930721	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930722	0.89[EUR][1000 genomes]
rs4930723	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4930724	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4930725	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4930726	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55990776	0.92[EUR][1000 genomes]
rs56041971	0.95[EUR][1000 genomes]
rs6488910	0.83[YRI][hapmap]
rs6488912	0.99[EUR][1000 genomes]
rs6488913	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6488914	0.92[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.90[EUR][1000 genomes]
rs7131882	0.98[EUR][1000 genomes]
rs7132655	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7133378	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7134121	0.96[EUR][1000 genomes]
rs7135314	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs71458830	0.95[EUR][1000 genomes]
rs7301953	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305864	1.00[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs7307053	0.92[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs7307277	1.00[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs7311233	0.92[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs7311969	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7312404	1.00[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs7955815	0.89[EUR][1000 genomes]
rs7958691	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7961449	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7966192	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7973683	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7975482	1.00[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs7978610	1.00[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs952632	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9863	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9971695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10846580	SRRM4	cis	parietal	SCAN
rs10846580	CCDC92	cis	cerebellum	SCAN
rs10846580	RP11-380L11.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124393800-124418000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:124394200-124418400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:124400400-124417800	Weak transcription	Spleen	Spleen
4	chr12:124407400-124422000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:124408400-124418000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:124408800-124428000	Weak transcription	Right Atrium	heart
7	chr12:124409400-124419600	Weak transcription	Right Ventricle	heart
8	chr12:124409600-124426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:124409800-124419400	Weak transcription	Brain Anterior Caudate	brain
10	chr12:124410000-124418600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:124410200-124418200	Weak transcription	Fetal Intestine Small	intestine
12	chr12:124410400-124420600	Weak transcription	Pancreas	Pancrea
13	chr12:124410800-124419200	Weak transcription	Brain Substantia Nigra	brain
14	chr12:124410800-124420600	Weak transcription	Brain Angular Gyrus	brain
15	chr12:124411200-124420600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:124411800-124416200	Strong transcription	Brain Germinal Matrix	brain
17	chr12:124412000-124420400	Enhancers	Fetal Thymus	thymus
18	chr12:124412400-124416200	Enhancers	Thymus	Thymus
19	chr12:124412800-124420400	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:124413000-124418800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:124413200-124418400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:124414000-124418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:124414600-124416600	Strong transcription	Fetal Brain Female	brain
24	chr12:124414800-124417800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:124415000-124416000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:124415000-124419000	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:124415000-124419000	Weak transcription	HSMMtube	muscle
28	chr12:124415000-124423000	Weak transcription	HSMM	muscle
29	chr12:124415200-124418200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:124415200-124419000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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