Variant report

Variant	rs10742816
Chromosome Location	chr11:47606984-47606985
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	POLR2A	chr11:47606406-47607164	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:47606498-47607087	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:47606758-47607061	GM12892	blood:	n/a	n/a
4	POLR2A	chr11:47606467-47608044	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr11:47606423-47607106	K562	blood:	n/a	n/a
6	POLR2A	chr11:47606504-47607088	GM12891	blood:	n/a	n/a
7	POLR2A	chr11:47606640-47607139	GM12892	blood:	n/a	n/a
8	POLR2A	chr11:47606635-47607004	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:47606438-47608201	K562	blood:	n/a	n/a
10	POLR2A	chr11:47606419-47607101	K562	blood:	n/a	n/a
11	POLR2A	chr11:47606800-47607009	K562	blood:	n/a	n/a
12	POLR2A	chr11:47606518-47607108	K562	blood:	n/a	n/a
13	POLR2A	chr11:47606464-47607008	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:47606828-47607027	GM12878	blood:	n/a	n/a
15	POLR2A	chr11:47606314-47607175	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
FAM180B	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1044269	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs10742805	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs10742806	0.94[JPT][hapmap]
rs11039300	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11819955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11821917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11824864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12419342	0.94[JPT][hapmap]
rs1474056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17198158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs17790804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17791016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs2138767	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2242511	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2869531	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs3740684	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs3824867	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs3847503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs4147730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4237544	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4282946	0.94[JPT][hapmap]
rs4752783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs4752786	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs4752837	0.94[JPT][hapmap]
rs4752839	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs4752843	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs4752848	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57828885	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58119589	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59837204	0.88[EUR][1000 genomes]
rs6485774	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs7105122	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7105907	0.94[JPT][hapmap]
rs7111873	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7115371	0.83[AMR][1000 genomes]
rs7116299	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7120737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7126210	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs753812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7931089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7944532	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7945911	0.89[EUR][1000 genomes]
rs7948705	0.94[JPT][hapmap]
rs7952204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9666924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10742816	SLC35C1	cis	cerebellum	SCAN
rs10742816	ATG13	cis	parietal	SCAN
rs10742816	LOC441601	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47601400-47611800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:47601400-47613400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47601800-47607000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:47601800-47607200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:47602000-47607000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:47602000-47607000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:47602000-47607000	Strong transcription	Fetal Lung	lung
8	chr11:47602000-47607200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:47602000-47607600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:47602000-47608000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:47602000-47608200	Strong transcription	Placenta	Placenta
12	chr11:47602200-47607000	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr11:47602200-47607000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:47602200-47607000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr11:47602200-47607000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:47602200-47607000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:47602200-47607000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:47602200-47607000	Strong transcription	Brain Substantia Nigra	brain
19	chr11:47602200-47607000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr11:47602200-47607000	Strong transcription	Rectal Smooth Muscle	rectum
21	chr11:47602200-47607000	Strong transcription	Right Ventricle	heart
22	chr11:47602200-47607000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:47602200-47607200	Strong transcription	Fetal Thymus	thymus
24	chr11:47602200-47607400	Strong transcription	Lung	lung
25	chr11:47602200-47607600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:47602200-47607600	Strong transcription	Fetal Intestine Large	intestine
27	chr11:47602200-47607800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:47602200-47607800	Strong transcription	Primary T cells from cord blood	blood
29	chr11:47602200-47608200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr11:47602200-47608200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:47602200-47608800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:47602200-47610400	Strong transcription	Fetal Brain Female	brain
33	chr11:47602400-47607000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:47602400-47607000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:47602400-47607000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:47602400-47607000	Strong transcription	Liver	Liver
37	chr11:47602400-47607000	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:47602400-47607200	Strong transcription	Brain Hippocampus Middle	brain
39	chr11:47602400-47607600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:47602400-47607600	Strong transcription	Brain Anterior Caudate	brain
41	chr11:47602400-47607600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr11:47602400-47607600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:47602400-47607800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:47602400-47608000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:47602400-47608200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:47602400-47608200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:47602400-47608400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:47602400-47609000	Strong transcription	Fetal Intestine Small	intestine
49	chr11:47602400-47609200	Strong transcription	Primary B cells from cord blood	blood
50	chr11:47602400-47609800	Strong transcription	Fetal Stomach	stomach

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