Variant report

Variant	rs10835613
Chromosome Location	chr11:4124276-4124277
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:4114277..4116935-chr11:4123036..4125551,3	K562	blood:

Variant related genes	Relation type
ENSG00000167325	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1015998	0.83[AMR][1000 genomes]
rs10835632	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835650	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11030907	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11030967	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11030976	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11030980	0.91[AMR][1000 genomes]
rs11031043	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11031070	0.83[AMR][1000 genomes]
rs11031096	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11604649	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12292367	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12364664	0.85[CEU][hapmap]
rs12803023	0.88[CHD][hapmap]
rs1372805	0.85[ASW][hapmap];0.88[CHD][hapmap];0.84[MEX][hapmap]
rs1662161	0.81[AMR][1000 genomes]
rs1662172	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1662173	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs183484	0.86[AMR][1000 genomes]
rs1980412	0.84[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs2119986	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284452	0.85[AMR][1000 genomes]
rs2304891	0.85[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.84[MEX][hapmap]
rs232054	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2412344	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2735689	0.86[AMR][1000 genomes]
rs2735691	0.84[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2920144	0.85[ASW][hapmap]
rs2959068	0.88[CHD][hapmap]
rs34356743	0.83[AMR][1000 genomes]
rs3794049	0.86[AMR][1000 genomes]
rs54816	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67074167	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7110060	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7124301	0.81[EUR][1000 genomes]
rs725518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs725519	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747883	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1053189	chr11:4123119-4359044	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10835613	OR52I2	cis	parietal	SCAN
rs10835613	KRTAP5-4	cis	cerebellum	SCAN
rs10835613	OR51E2	cis	cerebellum	SCAN
rs10835613	RRM1	cis	Artery Tibial	GTEx
rs10835613	TRIM21	cis	cerebellum	SCAN
rs10835613	RRM1	cis	cerebellum	SCAN
rs10835613	RRM1	cis	multi-tissue	Pritchard
rs10835613	TRIM5	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4117000-4124600	Weak transcription	Aorta	Aorta
2	chr11:4117000-4124600	Weak transcription	Left Ventricle	heart
3	chr11:4117000-4137200	Weak transcription	Esophagus	oesophagus
4	chr11:4117000-4141000	Weak transcription	Ovary	ovary
5	chr11:4117200-4126800	Weak transcription	Psoas Muscle	Psoas
6	chr11:4117200-4127400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:4117200-4142200	Weak transcription	Colonic Mucosa	Colon
8	chr11:4117400-4124600	Weak transcription	Lung	lung
9	chr11:4117400-4124600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:4117400-4125800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:4117400-4141800	Weak transcription	Small Intestine	intestine
12	chr11:4117600-4124600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:4117600-4124800	Weak transcription	Fetal Intestine Small	intestine
14	chr11:4117600-4125200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:4117600-4125800	Weak transcription	Liver	Liver
16	chr11:4117600-4126400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:4117600-4126400	Weak transcription	Fetal Intestine Large	intestine
18	chr11:4117600-4126600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:4117600-4126600	Weak transcription	Spleen	Spleen
20	chr11:4117600-4127000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:4117600-4127000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:4117600-4127200	Weak transcription	Brain Hippocampus Middle	brain
23	chr11:4117600-4127200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:4117600-4128600	Weak transcription	Brain Substantia Nigra	brain
25	chr11:4117600-4129200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:4117600-4129800	Weak transcription	Fetal Heart	heart
27	chr11:4117600-4133000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:4117600-4137400	Weak transcription	Right Ventricle	heart
29	chr11:4117600-4144600	Weak transcription	HSMMtube	muscle
30	chr11:4117600-4145200	Weak transcription	Gastric	stomach
31	chr11:4117600-4153000	Weak transcription	Stomach Mucosa	stomach
32	chr11:4117800-4124800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr11:4117800-4126400	Weak transcription	Brain Angular Gyrus	brain
34	chr11:4117800-4126400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr11:4117800-4126800	Weak transcription	NHLF	lung
36	chr11:4117800-4127000	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:4117800-4147800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr11:4117800-4160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:4118000-4125200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr11:4118000-4159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:4118400-4124800	Weak transcription	Pancreas	Pancrea
42	chr11:4118400-4125800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr11:4118400-4126200	Weak transcription	Fetal Lung	lung
44	chr11:4118400-4127000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:4118400-4146400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:4118400-4156200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:4118600-4124600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr11:4118600-4124600	Weak transcription	Fetal Stomach	stomach
49	chr11:4118600-4125800	Weak transcription	HUVEC	blood vessel
50	chr11:4118800-4126600	Weak transcription	NHEK	skin

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