Variant report

Variant	rs7040340
Chromosome Location	chr9:96443910-96443911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96442742..96446259-chr9:96719078..96722660,3	MCF-7	breast:
2	chr9:96443766..96445914-chr9:96765340..96767005,2	MCF-7	breast:
3	chr9:96443866..96445187-chr9:96726929..96728716,7	MCF-7	breast:
4	chr9:96443546..96446066-chr9:96715342..96717948,2	MCF-7	breast:
5	chr9:96443001..96444886-chr9:96710905..96713769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131668	Chromatin interaction
ENSG00000235601	Chromatin interaction

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

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

rs_ID	r²[population]
rs10117225	0.82[MEX][hapmap]
rs10122270	0.89[JPT][hapmap]
rs10123378	0.82[MEX][hapmap]
rs10761240	0.82[MEX][hapmap]
rs10761249	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10761250	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10821185	0.96[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs10821186	0.88[EUR][1000 genomes]
rs10821187	0.84[EUR][1000 genomes]
rs10821188	0.84[EUR][1000 genomes]
rs10821189	0.84[EUR][1000 genomes]
rs10821190	0.88[EUR][1000 genomes]
rs10821191	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs10821192	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs10821193	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10821194	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10821195	0.93[EUR][1000 genomes]
rs10821202	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821203	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10992797	0.82[MEX][hapmap]
rs10992812	0.88[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs10992813	0.84[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs10992815	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10992819	0.87[EUR][1000 genomes]
rs10992829	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992831	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992840	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992842	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992860	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1132004	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]
rs1140722	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11534279	0.92[CEU][hapmap]
rs12238738	0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1412048	0.91[MEX][hapmap]
rs1806524	0.92[CEU][hapmap]
rs2001315	0.83[EUR][1000 genomes]
rs2001589	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2001610	1.00[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2398848	1.00[CEU][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs2398856	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs34031628	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34103739	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35171420	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36013568	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750354	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3750357	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3750359	0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs3829758	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6479504	0.85[EUR][1000 genomes]
rs7036592	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7044244	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7851178	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7851271	0.84[EUR][1000 genomes]
rs7864397	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs7865712	0.89[JPT][hapmap]
rs7868191	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7871695	0.88[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
rs7040340	HIATL1	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96412600-96445000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:96413000-96444800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:96436800-96447000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:96437800-96444800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:96439600-96444800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:96439800-96444800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:96439800-96444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:96440200-96444400	Weak transcription	A549	lung
9	chr9:96440400-96444000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr9:96440400-96444200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:96440400-96444400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr9:96440400-96444800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:96440600-96444000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:96440600-96444400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr9:96440600-96444600	Weak transcription	Fetal Lung	lung
16	chr9:96440600-96444800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:96440600-96447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:96440800-96444000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:96440800-96444200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:96440800-96444400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr9:96440800-96444400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:96440800-96444600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:96440800-96444800	Weak transcription	Left Ventricle	heart
24	chr9:96440800-96445600	Weak transcription	NHLF	lung
25	chr9:96440800-96447400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:96441000-96444000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr9:96441000-96444000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr9:96441000-96444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:96441000-96444200	Weak transcription	Esophagus	oesophagus
30	chr9:96441000-96444400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:96441000-96446400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:96441000-96447200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:96441400-96444000	Weak transcription	Primary T cells from cord blood	blood
34	chr9:96441400-96444000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:96441400-96444400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:96441400-96444400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr9:96441400-96444600	Weak transcription	Colonic Mucosa	Colon
38	chr9:96442200-96446200	Weak transcription	Lung	lung
39	chr9:96442400-96444000	Weak transcription	Placenta	Placenta
40	chr9:96442400-96444200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:96442400-96444200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:96442400-96444400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:96442400-96444400	Weak transcription	Brain Germinal Matrix	brain
44	chr9:96442400-96444400	Weak transcription	Right Ventricle	heart
45	chr9:96442400-96446200	Weak transcription	Thymus	Thymus
46	chr9:96442400-96447400	Weak transcription	Adipose Nuclei	Adipose
47	chr9:96442400-96447600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:96442600-96444400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr9:96442600-96447600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr9:96442800-96449200	Weak transcription	Fetal Muscle Leg	muscle

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