Variant report

Variant	rs10991629
Chromosome Location	chr9:108094256-108094257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108091662..108093577-chr9:108093794..108096648,3	MCF-7	breast:
2	chr9:108093939..108096584-chr9:108118333..108121289,2	MCF-7	breast:
3	chr9:108093881..108095656-chr9:108101683..108104363,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10120853	0.82[LWK][hapmap]
rs10123494	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10820799	0.87[AFR][1000 genomes]
rs10820800	0.84[AFR][1000 genomes]
rs10820801	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10991624	0.91[AFR][1000 genomes]
rs10991628	0.97[AFR][1000 genomes]
rs10991639	1.00[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12350138	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350341	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs13294525	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13294539	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1410839	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2417614	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2417615	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2771033	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2771040	1.00[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28545469	0.82[AFR][1000 genomes]
rs3199966	0.86[MEX][hapmap]
rs34331578	0.88[AFR][1000 genomes]
rs34659648	1.00[ASN][1000 genomes]
rs34750132	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35603631	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4549843	0.84[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60502553	0.81[AFR][1000 genomes]
rs6479311	1.00[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6479313	0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479314	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479315	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479316	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7019052	1.00[ASN][1000 genomes]
rs7024985	1.00[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7029443	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7045091	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7856524	0.89[YRI][hapmap]
rs7863414	0.91[YRI][hapmap];0.91[AFR][1000 genomes]
rs7863781	0.83[AFR][1000 genomes]
rs7865985	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873937	1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs932006	0.96[YRI][hapmap];0.86[AFR][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	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10991629	CYLC2	cis	parietal	SCAN
rs10991629	OR13F1	cis	parietal	SCAN
rs10991629	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL
rs10991629	ZNF189	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108062200-108098800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr9:108062400-108098800	Weak transcription	Spleen	Spleen
4	chr9:108062400-108104600	Weak transcription	Right Ventricle	heart
5	chr9:108062600-108098600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:108062600-108098800	Weak transcription	Left Ventricle	heart
7	chr9:108062600-108098800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:108062800-108098400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr9:108062800-108098800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:108066200-108098600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr9:108068800-108098600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr9:108069000-108104000	Weak transcription	Fetal Heart	heart
13	chr9:108070400-108094600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:108071600-108099000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:108071800-108097800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:108072400-108098800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:108072600-108094800	Weak transcription	HSMMtube	muscle
18	chr9:108076000-108096200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:108078400-108101800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:108079600-108098800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:108080000-108098800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:108080400-108097800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr9:108081000-108123000	Weak transcription	Primary B cells from cord blood	blood
24	chr9:108081600-108096400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr9:108082000-108097600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:108082000-108098800	Weak transcription	Pancreas	Pancrea
27	chr9:108082200-108098600	Weak transcription	Primary T cells from cord blood	blood
28	chr9:108085000-108097800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr9:108087400-108098600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:108088400-108094800	Weak transcription	NH-A	brain
31	chr9:108089600-108097600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:108090000-108097800	Enhancers	Brain Substantia Nigra	brain
33	chr9:108090000-108098800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:108090400-108095600	Enhancers	Fetal Brain Male	brain
35	chr9:108090800-108108600	Weak transcription	Brain Germinal Matrix	brain
36	chr9:108091000-108097800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:108091200-108098600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr9:108091200-108098800	Weak transcription	Fetal Thymus	thymus
39	chr9:108091400-108094600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr9:108091400-108096400	Enhancers	HepG2	liver
41	chr9:108091400-108098600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:108091600-108097000	Enhancers	NHDF-Ad	bronchial
43	chr9:108091600-108097000	Enhancers	Osteobl	bone
44	chr9:108091600-108098600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr9:108091600-108103800	Weak transcription	Thymus	Thymus
46	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr9:108091800-108096600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:108091800-108097000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:108091800-108098800	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:108091800-108101400	Weak transcription	NHEK	skin

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