Variant report

Variant	rs1977288
Chromosome Location	chr10:96307738-96307739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:96304239..96306860-chr10:96307648..96309568,3	K562	blood:
2	chr10:96304195..96307318-chr10:96307648..96311886,5	K562	blood:
3	chr10:96306294..96309021-chr10:96316197..96318090,2	K562	blood:

Variant related genes	Relation type
ENSG00000119969	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

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	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10882477	1.00[JPT][hapmap]
rs11187930	0.80[EUR][1000 genomes]
rs11187939	1.00[JPT][hapmap]
rs11187940	0.95[CEU][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs11187944	1.00[JPT][hapmap]
rs11187952	1.00[JPT][hapmap]
rs11187960	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]
rs11188009	1.00[JPT][hapmap]
rs11188012	0.83[JPT][hapmap]
rs11188019	0.83[JPT][hapmap]
rs11188020	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188036	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11638	0.83[JPT][hapmap]
rs12221475	1.00[JPT][hapmap]
rs1326839	0.94[JPT][hapmap]
rs1334595	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]
rs1409655	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs1931757	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.82[EUR][1000 genomes]
rs1977291	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1980741	0.83[JPT][hapmap]
rs2031323	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2265366	0.81[EUR][1000 genomes]
rs2281791	1.00[JPT][hapmap]
rs2860840	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs3740358	1.00[JPT][hapmap]
rs3781262	1.00[JPT][hapmap]
rs4351744	0.83[JPT][hapmap]
rs4564258	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4600139	0.81[AMR][1000 genomes]
rs480032	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4918402	1.00[JPT][hapmap]
rs517784	1.00[JPT][hapmap]
rs556055	1.00[JPT][hapmap]
rs6583941	0.83[EUR][1000 genomes]
rs6583942	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6583947	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs692872	1.00[JPT][hapmap]
rs701885	1.00[JPT][hapmap]
rs7075182	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7078478	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7078811	0.83[JPT][hapmap]
rs7083898	0.83[JPT][hapmap]
rs7087798	0.86[ASW][hapmap];0.96[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7088008	0.82[EUR][1000 genomes]
rs7092129	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7096007	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7900007	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7906843	0.82[JPT][hapmap]
rs7913343	1.00[JPT][hapmap]
rs7921721	0.83[JPT][hapmap]
rs7922956	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9645542	0.83[AMR][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	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
2	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
3	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
rs1977288	HELLS	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96304400-96309000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr10:96304800-96307800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:96305800-96308000	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr10:96306200-96307800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
5	chr10:96306200-96318600	Weak transcription	Aorta	Aorta
6	chr10:96306400-96308000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
7	chr10:96306400-96308200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
8	chr10:96306400-96309400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
9	chr10:96306400-96309600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
10	chr10:96306400-96314200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr10:96306400-96314400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:96306400-96321200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:96306400-96325400	Weak transcription	Lung	lung
14	chr10:96306400-96330600	Weak transcription	Placenta	Placenta
15	chr10:96306400-96357200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr10:96306400-96365600	Weak transcription	Esophagus	oesophagus
17	chr10:96306400-96370400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr10:96306400-96370600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr10:96306400-96371000	Weak transcription	Ovary	ovary
20	chr10:96306600-96311600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr10:96306600-96314000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr10:96306600-96349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:96306600-96353800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr10:96306600-96379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:96306800-96309000	Weak transcription	Fetal Heart	heart
26	chr10:96306800-96310200	Weak transcription	Fetal Intestine Small	intestine
27	chr10:96306800-96314200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr10:96306800-96314200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr10:96306800-96314400	Weak transcription	Fetal Muscle Leg	muscle
30	chr10:96306800-96314600	Weak transcription	Thymus	Thymus
31	chr10:96306800-96315800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr10:96306800-96317200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr10:96306800-96317200	Weak transcription	Fetal Intestine Large	intestine
34	chr10:96306800-96318600	Weak transcription	HSMM	muscle
35	chr10:96306800-96323000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr10:96306800-96330400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:96306800-96348000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr10:96306800-96348200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr10:96306800-96348400	Weak transcription	Primary B cells from cord blood	blood
40	chr10:96306800-96349800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr10:96306800-96357200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr10:96306800-96373000	Weak transcription	Primary T cells from cord blood	blood
43	chr10:96307000-96307800	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:96307000-96307800	Enhancers	NHEK	skin
45	chr10:96307000-96308400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:96307000-96310000	Weak transcription	Fetal Stomach	stomach
47	chr10:96307000-96310200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr10:96307000-96312400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr10:96307000-96314400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:96307000-96314800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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