Variant report

Variant	rs1132004
Chromosome Location	chr9:96440808-96440809
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96420113..96421797-chr9:96439753..96442737,2	MCF-7	breast:
2	chr9:96434785..96437618-chr9:96438061..96441050,2	K562	blood:
3	chr9:96434498..96437281-chr9:96438650..96440857,2	MCF-7	breast:
4	chr9:96434785..96437496-chr9:96439550..96441266,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10117225	0.91[MEX][hapmap]
rs10122270	0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10123378	0.90[MEX][hapmap]
rs10761240	0.91[MEX][hapmap]
rs10761249	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10761250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821168	0.86[MEX][hapmap]
rs10821185	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821186	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10821187	0.86[EUR][1000 genomes]
rs10821188	0.86[EUR][1000 genomes]
rs10821189	0.86[EUR][1000 genomes]
rs10821190	0.90[EUR][1000 genomes]
rs10821191	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs10821192	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821193	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821194	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821195	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821202	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821203	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10992797	0.91[MEX][hapmap]
rs10992812	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs10992813	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992815	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992819	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992829	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992831	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992839	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992840	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992842	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992860	0.88[CEU][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1140722	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11534279	0.92[CEU][hapmap]
rs12238738	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1412048	0.81[MEX][hapmap]
rs1806524	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes]
rs2001315	0.85[EUR][1000 genomes]
rs2001589	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2001610	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2398848	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2398856	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs34031628	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34103739	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35171420	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36013568	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3750354	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3750357	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3750359	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829758	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479504	0.83[EUR][1000 genomes]
rs7036592	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7040340	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7044244	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7851178	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7851271	0.86[EUR][1000 genomes]
rs7864397	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs7865712	0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs7868191	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7871695	0.87[EUR][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	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1132004	HIATL1	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96412600-96442800	Weak transcription	NHDF-Ad	bronchial
2	chr9:96412600-96445000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:96412800-96442800	Weak transcription	HMEC	breast
4	chr9:96412800-96443600	Weak transcription	Stomach Mucosa	stomach
5	chr9:96413000-96442000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:96413000-96444800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:96413400-96441600	Weak transcription	GM12878-XiMat	blood
8	chr9:96416400-96443400	Weak transcription	HepG2	liver
9	chr9:96426000-96441800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:96426200-96442200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:96426400-96441600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:96431400-96441800	Weak transcription	K562	blood
13	chr9:96434200-96441000	Strong transcription	Pancreas	Pancrea
14	chr9:96434600-96441000	Strong transcription	Esophagus	oesophagus
15	chr9:96434600-96442400	Strong transcription	Fetal Intestine Small	intestine
16	chr9:96434600-96443200	Strong transcription	Fetal Stomach	stomach
17	chr9:96434800-96441400	Strong transcription	Primary T cells from cord blood	blood
18	chr9:96434800-96441400	Strong transcription	Brain Cingulate Gyrus	brain
19	chr9:96434800-96442400	Strong transcription	Placenta	Placenta
20	chr9:96435000-96441000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:96435000-96441000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:96435000-96441000	Strong transcription	Ovary	ovary
23	chr9:96435000-96441200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:96435000-96441200	Strong transcription	Adipose Nuclei	Adipose
25	chr9:96435000-96441400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr9:96435000-96441400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr9:96435000-96441400	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:96435000-96441600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr9:96435000-96442400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:96435000-96442400	Strong transcription	Thymus	Thymus
31	chr9:96435000-96442600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr9:96435000-96442800	Strong transcription	Fetal Muscle Leg	muscle
33	chr9:96435200-96441000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr9:96435200-96441000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr9:96435200-96441000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:96435200-96441000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:96435200-96441000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:96435200-96441000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr9:96435200-96441400	Strong transcription	Colonic Mucosa	Colon
40	chr9:96435200-96442400	Strong transcription	Brain Germinal Matrix	brain
41	chr9:96435200-96442600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr9:96435200-96442800	Strong transcription	Fetal Brain Female	brain
43	chr9:96435400-96441000	Strong transcription	Fetal Thymus	thymus
44	chr9:96435600-96442400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:96435800-96441000	Strong transcription	Spleen	Spleen
46	chr9:96436000-96441000	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr9:96436000-96441400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:96436000-96441400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:96436200-96441200	Strong transcription	Right Ventricle	heart
50	chr9:96436600-96442600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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