Variant report

Variant	rs1790246
Chromosome Location	chr11:77555356-77555357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77552027..77554925-chr11:77555085..77557941,2	K562	blood:

Variant related genes	Relation type
ENSG00000087884	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10698394	0.82[ASN][1000 genomes]
rs10793262	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10793263	0.86[ASN][1000 genomes]
rs10793264	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899398	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs10899402	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10899403	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10899405	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899406	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899407	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899408	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899409	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11237284	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11237289	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11237295	1.00[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237299	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11237303	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11237348	0.89[ASW][hapmap]
rs11518811	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12222530	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12364072	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1613945	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1783546	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790235	0.88[ASN][1000 genomes]
rs1790240	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1790250	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1793334	0.87[ASN][1000 genomes]
rs1793336	0.85[CHB][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs1793341	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1793343	0.89[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs2034499	1.00[ASW][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs2212317	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs2276441	0.85[CHB][hapmap]
rs2510967	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3018415	0.81[ASN][1000 genomes]
rs4245453	0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945198	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4945206	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs496786	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs61900164	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs630711	0.84[CHB][hapmap]
rs6592741	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs672460	0.88[ASW][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs7110670	0.89[ASW][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs7358471	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7925343	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7927913	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7931272	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7938133	0.89[ASW][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs7938648	0.85[CHB][hapmap]
rs9666484	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs9988883	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[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	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1790246	INTS4	cis	cerebellum	SCAN
rs1790246	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs1790246	INTS4	cis	parietal	SCAN
rs1790246	INT4	cis	multi-tissue	Pritchard
rs1790246	PAK1	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77533400-77565600	Weak transcription	Gastric	stomach
2	chr11:77533400-77565600	Weak transcription	Pancreas	Pancrea
3	chr11:77534600-77555400	Weak transcription	Lung	lung
4	chr11:77535400-77565600	Weak transcription	HepG2	liver
5	chr11:77544600-77555400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:77544600-77564400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:77544600-77565400	Weak transcription	Spleen	Spleen
8	chr11:77544800-77564400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:77544800-77565400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:77545000-77555400	Weak transcription	Fetal Kidney	kidney
11	chr11:77547200-77565800	Weak transcription	Fetal Heart	heart
12	chr11:77548800-77582800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:77550000-77565600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:77550400-77557200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:77550800-77564000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:77550800-77565400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:77551000-77555400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:77551200-77558400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:77551400-77565400	Weak transcription	Fetal Thymus	thymus
20	chr11:77551800-77556600	Strong transcription	Ovary	ovary
21	chr11:77552000-77555400	Strong transcription	Fetal Intestine Large	intestine
22	chr11:77552000-77555400	Strong transcription	Fetal Stomach	stomach
23	chr11:77552000-77560400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:77552000-77562600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:77552200-77555400	Strong transcription	Fetal Lung	lung
26	chr11:77552200-77556600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr11:77552200-77556800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:77552200-77557400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:77552200-77558600	Strong transcription	Brain Hippocampus Middle	brain
30	chr11:77552200-77562800	Strong transcription	Liver	Liver
31	chr11:77552200-77563000	Strong transcription	Left Ventricle	heart
32	chr11:77552200-77563600	Strong transcription	Adipose Nuclei	Adipose
33	chr11:77552200-77565800	Weak transcription	NHLF	lung
34	chr11:77552400-77555400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr11:77552600-77555800	Strong transcription	Brain Cingulate Gyrus	brain
36	chr11:77552600-77564400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:77552600-77565400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr11:77552600-77565400	Weak transcription	Thymus	Thymus
39	chr11:77552800-77558800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:77552800-77562200	Weak transcription	Small Intestine	intestine
41	chr11:77553000-77555400	Weak transcription	Fetal Intestine Small	intestine
42	chr11:77553000-77565000	Weak transcription	Right Ventricle	heart
43	chr11:77553000-77565600	Weak transcription	Aorta	Aorta
44	chr11:77553200-77565600	Weak transcription	Psoas Muscle	Psoas
45	chr11:77553400-77555400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:77553400-77555600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:77553400-77556200	Strong transcription	Primary T cells from cord blood	blood
48	chr11:77553600-77557600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:77553800-77555600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:77553800-77555800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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