Variant report

Variant	rs11187960
Chromosome Location	chr10:96217864-96217865
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	chr10:96207442..96209613-chr10:96216496..96219251,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10786168	1.00[JPT][hapmap]
rs10786169	0.83[JPT][hapmap]
rs10882455	1.00[LWK][hapmap]
rs10882460	1.00[JPT][hapmap]
rs10882463	1.00[JPT][hapmap]
rs10882474	1.00[JPT][hapmap]
rs10882475	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10882477	1.00[JPT][hapmap]
rs11187930	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11187938	0.83[ASN][1000 genomes]
rs11187939	1.00[JPT][hapmap]
rs11187940	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11187944	1.00[JPT][hapmap]
rs11187952	1.00[JPT][hapmap]
rs11188009	1.00[JPT][hapmap]
rs11188012	0.83[JPT][hapmap]
rs11188019	0.83[JPT][hapmap]
rs11188020	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11492628	0.81[ASN][1000 genomes]
rs11638	0.83[JPT][hapmap]
rs12221475	1.00[JPT][hapmap]
rs1326839	0.94[JPT][hapmap]
rs1334595	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17519764	1.00[LWK][hapmap]
rs1931757	0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1977288	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs1977291	0.92[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1980741	0.83[JPT][hapmap]
rs2031323	0.81[EUR][1000 genomes]
rs2265366	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2281791	1.00[JPT][hapmap]
rs2764378	0.83[AMR][1000 genomes]
rs3740358	1.00[JPT][hapmap]
rs3781262	1.00[JPT][hapmap]
rs4351744	0.83[JPT][hapmap]
rs4564258	0.81[EUR][1000 genomes]
rs480032	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4918402	1.00[JPT][hapmap]
rs517784	1.00[JPT][hapmap]
rs556055	1.00[JPT][hapmap]
rs6583941	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6583942	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs692872	1.00[JPT][hapmap]
rs701885	1.00[JPT][hapmap]
rs7075182	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes]
rs7078478	0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs7078811	0.83[JPT][hapmap]
rs7083898	0.83[JPT][hapmap]
rs7087798	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7088008	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7092129	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs7096007	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7393240	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7900007	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7906843	0.82[JPT][hapmap]
rs7913343	1.00[JPT][hapmap]
rs7921721	0.83[JPT][hapmap]
rs7922956	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9633675	0.90[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	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11187960	HELLS	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96190800-96234600	Weak transcription	Osteobl	bone
2	chr10:96198400-96218200	Weak transcription	Aorta	Aorta
3	chr10:96199400-96219600	Weak transcription	Pancreas	Pancrea
4	chr10:96200200-96219400	Weak transcription	Left Ventricle	heart
5	chr10:96201200-96219200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:96203000-96218600	Weak transcription	Ovary	ovary
7	chr10:96203000-96239600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr10:96203400-96242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:96203600-96218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:96203800-96219600	Weak transcription	Brain Angular Gyrus	brain
11	chr10:96204000-96221000	Weak transcription	Liver	Liver
12	chr10:96204200-96243400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:96206200-96218000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr10:96209000-96218400	Weak transcription	Lung	lung
15	chr10:96209600-96219600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:96210200-96248800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:96211400-96218200	Weak transcription	Fetal Intestine Large	intestine
18	chr10:96211600-96218000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr10:96211600-96218600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr10:96211600-96220800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:96211600-96224000	Weak transcription	Psoas Muscle	Psoas
22	chr10:96211600-96292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr10:96212000-96218400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:96212200-96218000	Weak transcription	Fetal Heart	heart
25	chr10:96212200-96219000	Weak transcription	Adipose Nuclei	Adipose
26	chr10:96212200-96219000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr10:96212200-96219400	Weak transcription	Fetal Kidney	kidney
28	chr10:96212400-96222800	Weak transcription	Fetal Lung	lung
29	chr10:96212600-96218000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr10:96212600-96248600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr10:96212800-96221000	Weak transcription	Brain Hippocampus Middle	brain
32	chr10:96213000-96222800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:96213000-96234400	Weak transcription	HSMM	muscle
34	chr10:96213800-96219000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr10:96215600-96255200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr10:96215800-96218000	Weak transcription	Fetal Stomach	stomach
37	chr10:96215800-96218200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr10:96215800-96218200	Weak transcription	Fetal Intestine Small	intestine
39	chr10:96215800-96219000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:96216200-96218000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:96216200-96219000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr10:96216400-96218000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr10:96216600-96223400	Weak transcription	Right Ventricle	heart
44	chr10:96216600-96243600	Weak transcription	Brain Anterior Caudate	brain
45	chr10:96216800-96221400	Weak transcription	Gastric	stomach
46	chr10:96217200-96218400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr10:96217200-96219200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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