Variant report

Variant	rs11726531
Chromosome Location	chr4:166211057-166211058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10015885	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10016520	0.80[ASN][1000 genomes]
rs10023176	0.80[ASN][1000 genomes]
rs10024370	0.89[ASN][1000 genomes]
rs10471096	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512319	0.82[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs16999615	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.80[LWK][hapmap];0.84[ASN][1000 genomes]
rs17842697	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.80[LWK][hapmap];0.85[ASN][1000 genomes]
rs17842699	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.80[LWK][hapmap]
rs28575657	0.84[ASN][1000 genomes]
rs3817246	0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3901797	0.85[ASN][1000 genomes]
rs4690809	0.87[ASN][1000 genomes]
rs4691180	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6536902	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6536903	0.85[CEU][hapmap];0.90[MEX][hapmap]
rs6828824	0.82[CEU][hapmap];0.90[MEX][hapmap]
rs6830714	0.91[CHB][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.81[YRI][hapmap]
rs7662569	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7685245	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs7692029	0.82[ASN][1000 genomes]
rs7698056	0.82[CEU][hapmap];0.89[MEX][hapmap]
rs7699872	0.88[ASN][1000 genomes]
rs9994064	0.80[ASN][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	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11726531	INTS12	trans	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166144600-166218800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:166177200-166218800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:166177400-166215200	Weak transcription	Fetal Stomach	stomach
4	chr4:166177400-166216000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:166177400-166218600	Weak transcription	Spleen	Spleen
6	chr4:166177400-166219000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:166178800-166218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:166178800-166218800	Weak transcription	Esophagus	oesophagus
9	chr4:166183800-166215200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:166183800-166218800	Weak transcription	Aorta	Aorta
11	chr4:166192800-166223000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:166195000-166215800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:166196200-166215800	Weak transcription	Left Ventricle	heart
14	chr4:166196200-166217600	Weak transcription	Gastric	stomach
15	chr4:166197600-166216000	Weak transcription	Pancreas	Pancrea
16	chr4:166198200-166230000	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:166199600-166223000	Weak transcription	Ovary	ovary
18	chr4:166200200-166217200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr4:166201000-166217200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:166202400-166218800	Weak transcription	Brain Germinal Matrix	brain
21	chr4:166204200-166223000	Weak transcription	Thymus	Thymus
22	chr4:166204800-166221200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:166205600-166218800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:166206000-166218800	Weak transcription	Fetal Intestine Small	intestine
25	chr4:166206200-166215400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:166206200-166216600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:166206200-166218600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:166208000-166217400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:166208800-166215200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:166209000-166215200	Weak transcription	Primary T cells from cord blood	blood
31	chr4:166209000-166215400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:166210000-166215400	Weak transcription	Brain Substantia Nigra	brain
33	chr4:166210200-166215000	Weak transcription	Primary B cells from cord blood	blood
34	chr4:166210200-166215400	Weak transcription	Brain Anterior Caudate	brain
35	chr4:166210200-166215400	Weak transcription	Fetal Lung	lung
36	chr4:166210200-166216000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:166210200-166218600	Weak transcription	HepG2	liver
38	chr4:166210200-166222800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:166210400-166211800	Weak transcription	Lung	lung
40	chr4:166210400-166212600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr4:166210400-166213400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr4:166210400-166215000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr4:166210400-166215200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:166210400-166215200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:166210400-166215200	Weak transcription	Adipose Nuclei	Adipose
46	chr4:166210400-166215200	Weak transcription	GM12878-XiMat	blood
47	chr4:166210400-166215600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:166210400-166215600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:166210400-166215800	Weak transcription	Brain Angular Gyrus	brain
50	chr4:166210400-166216000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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