Variant report

Variant	rs1334595
Chromosome Location	chr10:96250651-96250652
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	chr10:96249261..96251407-chr10:96253951..96256386,2	K562	blood:
2	chr10:96249542..96251929-chr10:96303686..96306611,2	K562	blood:

Variant related genes	Relation type
ENSG00000119969	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10786168	1.00[JPT][hapmap]
rs10786169	0.83[JPT][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];0.83[ASN][1000 genomes]
rs10882477	1.00[JPT][hapmap]
rs11187930	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11187939	1.00[JPT][hapmap]
rs11187940	0.95[CEU][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11187944	1.00[JPT][hapmap]
rs11187952	1.00[JPT][hapmap]
rs11187960	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]
rs11188009	1.00[JPT][hapmap]
rs11188012	0.83[JPT][hapmap]
rs11188019	0.83[JPT][hapmap]
rs11188020	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11638	0.83[JPT][hapmap]
rs12221475	1.00[JPT][hapmap]
rs1326839	0.94[JPT][hapmap]
rs1931757	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1977288	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1977291	0.86[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1980741	0.83[JPT][hapmap]
rs2031323	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2265366	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2281791	1.00[JPT][hapmap]
rs2764378	0.85[AMR][1000 genomes]
rs3740358	1.00[JPT][hapmap]
rs3781262	1.00[JPT][hapmap]
rs4351744	0.83[JPT][hapmap]
rs4564258	0.80[EUR][1000 genomes]
rs480032	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4918402	1.00[JPT][hapmap]
rs517784	1.00[JPT][hapmap]
rs556055	1.00[JPT][hapmap]
rs6583941	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6583942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583947	0.80[ASN][1000 genomes]
rs692872	1.00[JPT][hapmap]
rs701885	1.00[JPT][hapmap]
rs7075182	0.87[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap]
rs7078478	1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7078811	0.83[JPT][hapmap]
rs7083898	0.83[JPT][hapmap]
rs7087798	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7088008	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7092129	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs7096007	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7393240	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7900007	0.89[AFR][1000 genomes];0.96[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];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9633675	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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
rs1334595	HELLS	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96211600-96292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:96215600-96255200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr10:96219800-96283400	Weak transcription	Lung	lung
4	chr10:96221800-96255600	Weak transcription	Ovary	ovary
5	chr10:96222800-96255800	Weak transcription	HepG2	liver
6	chr10:96223200-96293600	Weak transcription	NHDF-Ad	bronchial
7	chr10:96227800-96255600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:96235000-96255200	Weak transcription	Osteobl	bone
9	chr10:96236000-96254400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:96236400-96268600	Weak transcription	HSMMtube	muscle
11	chr10:96237600-96258800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr10:96237600-96271400	Weak transcription	Placenta	Placenta
13	chr10:96238200-96258400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr10:96238200-96273400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr10:96240200-96271000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr10:96243800-96251600	Weak transcription	HSMM	muscle
17	chr10:96244000-96253200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:96244000-96255800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:96244000-96262200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr10:96244000-96282600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr10:96244400-96258400	Weak transcription	Fetal Stomach	stomach
22	chr10:96244400-96283600	Weak transcription	Pancreas	Pancrea
23	chr10:96244400-96304600	Weak transcription	Aorta	Aorta
24	chr10:96245200-96267000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr10:96246800-96261400	Weak transcription	Fetal Intestine Large	intestine
26	chr10:96247400-96267400	Weak transcription	Fetal Muscle Leg	muscle
27	chr10:96248000-96273800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr10:96248600-96250800	Enhancers	Brain Hippocampus Middle	brain
29	chr10:96248600-96251000	Enhancers	Brain Substantia Nigra	brain
30	chr10:96248800-96251000	Enhancers	Brain Anterior Caudate	brain
31	chr10:96248800-96256000	Weak transcription	Liver	Liver
32	chr10:96249000-96255600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr10:96249000-96267800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr10:96249200-96253200	Weak transcription	Fetal Intestine Small	intestine
35	chr10:96249200-96255600	Weak transcription	Psoas Muscle	Psoas
36	chr10:96249200-96267400	Weak transcription	Left Ventricle	heart
37	chr10:96249200-96286200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr10:96249400-96268600	Weak transcription	Colon Smooth Muscle	Colon
39	chr10:96249400-96288600	Weak transcription	Gastric	stomach
40	chr10:96249600-96267800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:96249800-96251600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr10:96250200-96250800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr10:96250200-96250800	Enhancers	Fetal Lung	lung
44	chr10:96250400-96250800	Enhancers	Brain Angular Gyrus	brain
45	chr10:96250400-96251000	Enhancers	Adipose Nuclei	Adipose
46	chr10:96250400-96281000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr10:96250600-96250800	Enhancers	Small Intestine	intestine
48	chr10:96250600-96251000	Enhancers	Fetal Heart	heart
49	chr10:96250600-96251200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr10:96250600-96256000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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