Variant report

Variant	rs11790431
Chromosome Location	chr9:103046916-103046917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103037852..103042243-chr9:103042555..103047658,4	K562	blood:
2	chr9:103039312..103042243-chr9:103045251..103047658,2	K562	blood:

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10512269	1.00[CHB][hapmap]
rs10760722	1.00[CHB][hapmap];0.81[MKK][hapmap]
rs10819725	1.00[CHB][hapmap]
rs10819726	1.00[CHB][hapmap]
rs10819727	1.00[CHB][hapmap]
rs10819730	1.00[CHB][hapmap]
rs10819747	1.00[CHB][hapmap];0.83[MKK][hapmap]
rs10819748	1.00[CHB][hapmap]
rs10819755	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs10819757	0.97[EUR][1000 genomes]
rs10819758	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs10819760	0.97[EUR][1000 genomes]
rs10819765	0.89[EUR][1000 genomes]
rs10819766	0.90[EUR][1000 genomes]
rs10819768	0.89[EUR][1000 genomes]
rs10819771	0.82[CEU][hapmap]
rs10819772	0.82[CEU][hapmap]
rs10988967	1.00[CHB][hapmap]
rs10988977	1.00[CHB][hapmap]
rs10988978	1.00[CHB][hapmap]
rs10988984	1.00[CHB][hapmap]
rs10988988	1.00[CHB][hapmap]
rs10988989	1.00[CHB][hapmap]
rs10988993	1.00[CHB][hapmap]
rs10988994	1.00[CHB][hapmap]
rs10988996	1.00[CHB][hapmap]
rs10989003	1.00[CHB][hapmap]
rs10989007	1.00[CHB][hapmap]
rs10989010	1.00[CHB][hapmap]
rs10989013	1.00[CHB][hapmap]
rs10989017	1.00[CHB][hapmap]
rs10989018	1.00[CHB][hapmap];0.82[MKK][hapmap]
rs10989019	1.00[CHB][hapmap]
rs10989020	1.00[CHB][hapmap]
rs10989041	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989047	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10989050	0.97[EUR][1000 genomes]
rs10989051	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs10989062	0.92[EUR][1000 genomes]
rs10989063	0.91[EUR][1000 genomes]
rs10989068	0.90[EUR][1000 genomes]
rs10989069	0.90[EUR][1000 genomes]
rs10989072	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs10989074	0.89[CEU][hapmap]
rs11515449	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11515542	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788648	0.97[EUR][1000 genomes]
rs11789482	1.00[CHB][hapmap]
rs11791943	0.85[EUR][1000 genomes]
rs11795004	0.90[EUR][1000 genomes]
rs11998890	1.00[CHB][hapmap]
rs12000794	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs12002124	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs12003061	1.00[CHB][hapmap]
rs12003124	1.00[CHB][hapmap]
rs12003468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005177	0.96[EUR][1000 genomes]
rs12377746	1.00[CHB][hapmap]
rs12379480	0.85[EUR][1000 genomes]
rs13284601	0.82[GIH][hapmap]
rs1338120	1.00[CHB][hapmap]
rs1415927	1.00[CHB][hapmap]
rs1529195	1.00[CHB][hapmap]
rs16919002	1.00[CHB][hapmap]
rs16919015	1.00[CHB][hapmap]
rs16919019	1.00[CHB][hapmap]
rs16919024	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919111	1.00[JPT][hapmap]
rs2416986	1.00[CHB][hapmap]
rs3199998	0.97[EUR][1000 genomes]
rs41274951	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41274961	0.92[EUR][1000 genomes]
rs6479004	1.00[CHB][hapmap]
rs6479006	1.00[CHB][hapmap]
rs7020780	1.00[CHB][hapmap];0.83[MKK][hapmap]
rs7021923	1.00[CHB][hapmap]
rs7025271	1.00[CHB][hapmap]
rs7026567	1.00[CHB][hapmap]
rs7028101	0.98[EUR][1000 genomes]
rs7028564	1.00[CHB][hapmap]
rs7029342	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs7033350	1.00[CHB][hapmap]
rs7036972	0.97[EUR][1000 genomes]
rs7037122	0.97[EUR][1000 genomes]
rs7037419	0.92[EUR][1000 genomes]
rs7039994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041818	1.00[CHB][hapmap]
rs7047193	1.00[CHB][hapmap]
rs7047693	1.00[CHB][hapmap]
rs7350268	1.00[CHB][hapmap]
rs7849019	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs7849323	1.00[CHB][hapmap]
rs7853497	1.00[CHB][hapmap]
rs7853561	1.00[CHB][hapmap]
rs7853585	1.00[CHB][hapmap]
rs7853672	1.00[CHB][hapmap]
rs7854689	1.00[CHB][hapmap]
rs7856932	1.00[CHB][hapmap]
rs7857556	1.00[CHB][hapmap]
rs7858045	1.00[CHB][hapmap]
rs7860268	1.00[CHB][hapmap]
rs7860660	1.00[CHB][hapmap]
rs7862614	1.00[CHB][hapmap];0.83[MKK][hapmap]
rs7865483	1.00[CHB][hapmap]
rs7866669	1.00[CHB][hapmap]
rs7866700	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866950	1.00[CHB][hapmap]
rs7868020	1.00[CHB][hapmap]
rs7868446	1.00[CHB][hapmap]
rs7868632	1.00[CHB][hapmap]
rs7870469	1.00[CHB][hapmap]
rs7870701	1.00[CHB][hapmap]
rs7872897	1.00[CHB][hapmap]
rs7873560	0.90[EUR][1000 genomes]
rs7874036	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1835721	chr9:102991314-103096666	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11790431	TMOD1	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102973000-103053800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:102974000-103047600	Weak transcription	Fetal Brain Male	brain
3	chr9:102976800-103047800	Weak transcription	Fetal Heart	heart
4	chr9:102979400-103054600	Weak transcription	NHEK	skin
5	chr9:102987400-103054600	Weak transcription	Gastric	stomach
6	chr9:102989400-103047200	Weak transcription	GM12878-XiMat	blood
7	chr9:102997800-103054400	Weak transcription	Colonic Mucosa	Colon
8	chr9:103009400-103047600	Weak transcription	HUVEC	blood vessel
9	chr9:103013000-103047400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:103016000-103047200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:103022000-103047800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:103026200-103047600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:103029000-103053600	Weak transcription	Hela-S3	cervix
14	chr9:103029200-103047000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr9:103029200-103047600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:103029200-103054600	Weak transcription	Brain Angular Gyrus	brain
17	chr9:103029800-103047400	Weak transcription	HepG2	liver
18	chr9:103034200-103047200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:103034800-103047400	Strong transcription	Primary T cells from cord blood	blood
20	chr9:103035000-103047200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:103039000-103047400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr9:103039400-103047800	Weak transcription	HSMMtube	muscle
23	chr9:103040200-103047000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:103040200-103047600	Weak transcription	HSMM	muscle
25	chr9:103040400-103053000	Weak transcription	NHLF	lung
26	chr9:103040400-103058600	Weak transcription	NH-A	brain
27	chr9:103040800-103047800	Weak transcription	NHDF-Ad	bronchial
28	chr9:103041400-103047600	Strong transcription	Liver	Liver
29	chr9:103042400-103047400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:103043400-103047200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:103044000-103047200	Strong transcription	Thymus	Thymus
32	chr9:103044000-103067800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:103044200-103048200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:103044200-103048800	Strong transcription	Left Ventricle	heart
35	chr9:103044200-103071200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:103044600-103102400	Weak transcription	Stomach Mucosa	stomach
37	chr9:103044800-103049600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:103044800-103067800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr9:103045200-103047600	Weak transcription	K562	blood
40	chr9:103045200-103053000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:103045800-103047200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:103045800-103047600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr9:103045800-103047800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:103045800-103047800	Strong transcription	Ovary	ovary
45	chr9:103045800-103050800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:103045800-103051200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr9:103045800-103051200	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr9:103045800-103052000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:103045800-103052000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:103045800-103052200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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