Variant report

Variant	rs3118756
Chromosome Location	chr9:97047402-97047403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97040959..97043614-chr9:97043619..97047501,3	K562	blood:

Variant related genes	Relation type
ENSG00000175787	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10821325	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs10821326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.84[ASN][1000 genomes]
rs12338655	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16912862	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1971396	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2479601	0.84[CEU][hapmap]
rs2479602	0.84[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs3118753	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3118754	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3118761	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3118762	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3118765	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3131899	0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3131901	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131902	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131904	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131910	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]
rs4744346	0.84[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs6479533	0.92[ASN][1000 genomes]
rs6479534	0.92[ASN][1000 genomes]
rs6479537	0.82[CHB][hapmap]
rs688165	0.84[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs7027606	0.81[JPT][hapmap]
rs7031496	0.84[CEU][hapmap]
rs7041842	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7848227	0.82[CEU][hapmap]
rs7857240	0.83[ASN][1000 genomes]
rs9299422	0.83[CHB][hapmap]
rs9409511	0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9409512	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9409513	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9409514	0.81[AMR][1000 genomes]
rs9409718	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9409759	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs9695176	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9696843	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[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	nsv968732	chr9:97043511-97050792	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3118756	HIATL1	cis	multi-tissue	Pritchard
rs3118756	FANCC	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97022200-97055200	Weak transcription	Aorta	Aorta
2	chr9:97022600-97055200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:97022800-97054600	Weak transcription	Pancreas	Pancrea
4	chr9:97023000-97050000	Weak transcription	Right Ventricle	heart
5	chr9:97023000-97055400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:97030200-97048400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:97031800-97050400	Weak transcription	Psoas Muscle	Psoas
8	chr9:97032400-97064600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:97033600-97054600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:97036800-97062600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:97037400-97050200	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:97039200-97053600	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:97039200-97055000	Weak transcription	Brain Substantia Nigra	brain
14	chr9:97039200-97062600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:97039400-97054600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:97039400-97067600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:97040000-97064600	Weak transcription	Brain Germinal Matrix	brain
18	chr9:97041200-97048400	Weak transcription	NH-A	brain
19	chr9:97041200-97050000	Weak transcription	Gastric	stomach
20	chr9:97041200-97051600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:97041200-97054400	Weak transcription	NHDF-Ad	bronchial
22	chr9:97041200-97054600	Weak transcription	Stomach Mucosa	stomach
23	chr9:97041200-97065400	Weak transcription	Small Intestine	intestine
24	chr9:97041400-97050000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:97041400-97053600	Weak transcription	HepG2	liver
26	chr9:97041800-97054800	Weak transcription	Fetal Brain Male	brain
27	chr9:97042200-97054400	Weak transcription	Spleen	Spleen
28	chr9:97042200-97055400	Weak transcription	Esophagus	oesophagus
29	chr9:97042400-97050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:97042400-97050600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:97042600-97061400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr9:97042600-97068400	Weak transcription	Fetal Brain Female	brain
33	chr9:97042800-97049800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:97042800-97050200	Weak transcription	HSMMtube	muscle
35	chr9:97042800-97050600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr9:97042800-97054600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:97042800-97054600	Weak transcription	Fetal Kidney	kidney
38	chr9:97042800-97057000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:97042800-97064000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr9:97042800-97064400	Weak transcription	Hela-S3	cervix
41	chr9:97043000-97049000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:97043000-97050800	Weak transcription	NHEK	skin
43	chr9:97043000-97051200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr9:97043000-97053600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:97043000-97053600	Weak transcription	Brain Anterior Caudate	brain
46	chr9:97043000-97054200	Weak transcription	Osteobl	bone
47	chr9:97043000-97057000	Weak transcription	HUVEC	blood vessel
48	chr9:97043000-97061400	Weak transcription	Fetal Thymus	thymus
49	chr9:97043200-97048200	Weak transcription	Liver	Liver
50	chr9:97043200-97048600	Weak transcription	Adipose Nuclei	Adipose

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