Variant report

Variant	rs3131910
Chromosome Location	chr9:97056183-97056184
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97054703..97056976-chr9:97060174..97062566,2	MCF-7	breast:
2	chr9:97021120..97022711-chr9:97055563..97058040,2	K562	blood:
3	chr9:97011802..97014770-chr9:97055516..97058379,2	K562	blood:

Variant related genes	Relation type
ENSG00000175787	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10821325	0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap]
rs10821326	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap]
rs12338655	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16912862	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1752786	0.85[CHB][hapmap]
rs1971396	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2277182	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2479601	0.88[CEU][hapmap]
rs2479602	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap]
rs2769119	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs3118753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3118754	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3118756	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3118761	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3118762	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3118765	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3131899	0.86[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs3131901	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131902	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131904	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4477096	0.86[CHB][hapmap]
rs4744346	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap]
rs59717415	0.87[ASN][1000 genomes]
rs6479533	0.87[ASN][1000 genomes]
rs6479534	0.87[ASN][1000 genomes]
rs6479537	0.90[CHB][hapmap]
rs684892	0.86[CHB][hapmap]
rs688165	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap]
rs7025755	0.86[CHB][hapmap]
rs7031088	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs7031496	0.88[CEU][hapmap]
rs7041842	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7848227	0.87[CEU][hapmap];0.89[CHB][hapmap]
rs7857240	0.88[ASN][1000 genomes]
rs9299422	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs9409511	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9409512	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409513	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9409514	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9409718	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9409759	0.87[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs9409765	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs9695176	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9696843	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.87[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	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3131910	HIATL1	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97032400-97064600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:97036800-97062600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:97039200-97062600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:97039400-97067600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:97040000-97064600	Weak transcription	Brain Germinal Matrix	brain
6	chr9:97041200-97065400	Weak transcription	Small Intestine	intestine
7	chr9:97042600-97061400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:97042600-97068400	Weak transcription	Fetal Brain Female	brain
9	chr9:97042800-97057000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:97042800-97064000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:97042800-97064400	Weak transcription	Hela-S3	cervix
12	chr9:97043000-97057000	Weak transcription	HUVEC	blood vessel
13	chr9:97043000-97061400	Weak transcription	Fetal Thymus	thymus
14	chr9:97043200-97060000	Weak transcription	Fetal Lung	lung
15	chr9:97043200-97062800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:97043200-97062800	Weak transcription	Brain Angular Gyrus	brain
17	chr9:97043200-97063000	Weak transcription	HMEC	breast
18	chr9:97043200-97064000	Weak transcription	Colonic Mucosa	Colon
19	chr9:97043200-97064400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:97043800-97059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr9:97043800-97066400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:97044000-97059800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr9:97044000-97062600	Weak transcription	A549	lung
24	chr9:97046000-97063600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr9:97047000-97059200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr9:97048200-97059000	Strong transcription	Primary B cells from cord blood	blood
27	chr9:97048400-97060600	Strong transcription	Primary T cells from cord blood	blood
28	chr9:97048800-97058000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:97049600-97061000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:97050600-97062600	Weak transcription	Right Atrium	heart
31	chr9:97050800-97064600	Weak transcription	Right Ventricle	heart
32	chr9:97051000-97057400	Weak transcription	Psoas Muscle	Psoas
33	chr9:97051000-97061200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:97051600-97061400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:97052600-97064200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr9:97053400-97060200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:97053600-97058400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:97053600-97058400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr9:97053800-97057000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr9:97053800-97063400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr9:97054000-97056400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:97054000-97057200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr9:97054000-97058400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:97054000-97059800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr9:97054000-97060400	Weak transcription	K562	blood
46	chr9:97054200-97056400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:97054200-97056600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr9:97054200-97056600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr9:97054200-97057000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr9:97054200-97058000	Strong transcription	Duodenum Smooth Muscle	Duodenum

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