Variant report

Variant	rs2001610
Chromosome Location	chr9:96395429-96395430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96394612..96397512-chr9:96407900..96409512,2	MCF-7	breast:
2	chr9:96393648..96395801-chr9:96402500..96404793,2	MCF-7	breast:
3	chr9:96394493..96396202-chr9:96397169..96399120,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10117225	0.86[MEX][hapmap]
rs10122270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10123378	0.86[MEX][hapmap]
rs10761240	0.86[MEX][hapmap]
rs10761249	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10761250	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821168	0.82[MEX][hapmap]
rs10821185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821186	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821187	0.94[EUR][1000 genomes]
rs10821188	0.94[EUR][1000 genomes]
rs10821189	0.94[EUR][1000 genomes]
rs10821190	0.91[EUR][1000 genomes]
rs10821191	1.00[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs10821192	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821193	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821194	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821195	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821202	0.86[EUR][1000 genomes]
rs10821203	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992797	0.86[MEX][hapmap]
rs10992812	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992813	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992815	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992819	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992829	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992831	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992842	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10992860	0.88[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1132004	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]
rs1140722	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11534279	0.92[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs12238738	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1806524	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2001315	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2001589	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.85[LWK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2398848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2398856	1.00[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs34031628	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34103739	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35171420	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36013568	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3750354	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3750357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3750359	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3829758	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7036592	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7040340	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]
rs7044244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7851178	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7851271	0.94[EUR][1000 genomes]
rs7864397	1.00[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs7865712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7868191	0.95[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040891	chr9:96361529-96397338	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1044461	chr9:96362048-96397338	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv893585	chr9:96363859-96403367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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
5	nsv1055035	chr9:96372269-96402747	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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
7	nsv519449	chr9:96382100-96395429	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	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
rs2001610	HIATL1	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96374600-96399800	Weak transcription	K562	blood
2	chr9:96380200-96411800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:96380800-96399800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:96384000-96396400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:96384600-96412200	Weak transcription	Stomach Mucosa	stomach
6	chr9:96387000-96411800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:96387200-96399800	Weak transcription	Fetal Heart	heart
8	chr9:96387600-96399600	Weak transcription	Fetal Kidney	kidney
9	chr9:96390200-96398800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:96390200-96405400	Weak transcription	HepG2	liver
11	chr9:96390400-96398600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:96390400-96399400	Weak transcription	Hela-S3	cervix
13	chr9:96390600-96397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:96390600-96398200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:96390600-96398400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:96390600-96399000	Weak transcription	Osteobl	bone
17	chr9:96390600-96399600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:96390800-96396800	Weak transcription	NHEK	skin
19	chr9:96390800-96398400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:96390800-96398600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr9:96391400-96398800	Strong transcription	Fetal Intestine Small	intestine
22	chr9:96391400-96400800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr9:96391600-96395800	Strong transcription	Fetal Thymus	thymus
24	chr9:96391600-96398400	Strong transcription	Thymus	Thymus
25	chr9:96391600-96398600	Strong transcription	Fetal Intestine Large	intestine
26	chr9:96391600-96398800	Strong transcription	Aorta	Aorta
27	chr9:96391600-96399600	Strong transcription	Primary T cells from cord blood	blood
28	chr9:96391600-96399800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr9:96391600-96400200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:96391600-96400200	Strong transcription	Gastric	stomach
31	chr9:96391600-96402000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr9:96391800-96398800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:96391800-96399000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:96391800-96399000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:96391800-96400000	Strong transcription	Colonic Mucosa	Colon
36	chr9:96391800-96400400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:96391800-96400400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:96391800-96402400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:96391800-96402400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:96391800-96402400	Strong transcription	Placenta	Placenta
41	chr9:96392000-96396800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:96392000-96396800	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr9:96392000-96397000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:96392000-96397200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:96392000-96397200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:96392000-96397400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:96392000-96398000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr9:96392000-96398200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:96392000-96398200	Strong transcription	Dnd41	blood
50	chr9:96392000-96398800	Strong transcription	Monocytes-CD14+_RO01746	blood

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