Variant report

Variant	rs10991639
Chromosome Location	chr9:108117571-108117572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:108117199-108118749	PBDE	blood:	n/a	n/a

Variant related genes	Relation type
SLC44A1	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10123494	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491810	1.00[ASN][1000 genomes]
rs10820801	1.00[CEU][hapmap];0.96[GIH][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10991629	1.00[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12339823	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12340765	1.00[ASN][1000 genomes]
rs12342542	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12344130	1.00[ASN][1000 genomes]
rs12350138	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs13294525	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13294539	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410837	1.00[ASN][1000 genomes]
rs1410839	0.94[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553870	1.00[ASN][1000 genomes]
rs1553873	1.00[ASN][1000 genomes]
rs16924529	1.00[ASN][1000 genomes]
rs16924530	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17246524	1.00[ASN][1000 genomes]
rs17305886	1.00[ASN][1000 genomes]
rs17305963	1.00[ASN][1000 genomes]
rs2417615	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2771031	1.00[ASN][1000 genomes]
rs2771033	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2771040	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812314	1.00[ASN][1000 genomes]
rs2812316	1.00[ASN][1000 genomes]
rs3199966	0.94[ASW][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34750132	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35603631	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296093	1.00[ASN][1000 genomes]
rs4549843	0.82[ASW][hapmap];0.83[CEU][hapmap];0.96[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6479311	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479313	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6479314	1.00[CEU][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6479315	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6479316	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7024985	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029443	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7045091	1.00[CEU][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724069	1.00[ASN][1000 genomes]
rs7858401	1.00[ASN][1000 genomes]
rs7865985	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7873937	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs907230	1.00[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][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	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	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
3	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
rs10991639	CYLC2	cis	parietal	SCAN
rs10991639	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL
rs10991639	ZNF189	cis	cerebellum	SCAN
rs10991639	OR13F1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108081000-108123000	Weak transcription	Primary B cells from cord blood	blood
3	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:108092000-108124000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:108092000-108148000	Weak transcription	Psoas Muscle	Psoas
6	chr9:108093200-108123200	Weak transcription	Colonic Mucosa	Colon
7	chr9:108093200-108149800	Weak transcription	HUVEC	blood vessel
8	chr9:108095600-108122200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:108096400-108131800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr9:108097000-108122800	Weak transcription	Fetal Kidney	kidney
12	chr9:108097200-108124600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:108097400-108133600	Weak transcription	Placenta	Placenta
14	chr9:108097600-108147000	Weak transcription	HMEC	breast
15	chr9:108099200-108122200	Weak transcription	Lung	lung
16	chr9:108099200-108123400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:108099200-108123800	Weak transcription	Aorta	Aorta
18	chr9:108099600-108122200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:108100200-108123000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:108100200-108123400	Weak transcription	Fetal Stomach	stomach
21	chr9:108100200-108136200	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:108100200-108149600	Weak transcription	Pancreas	Pancrea
23	chr9:108100400-108122200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr9:108100600-108123400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:108101000-108121600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:108101000-108122200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:108104800-108120200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:108104800-108122800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:108104800-108124000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:108104800-108124200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:108104800-108129600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:108104800-108147600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:108105000-108122200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:108105000-108122200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:108105000-108122400	Weak transcription	HSMM	muscle
36	chr9:108105000-108122800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:108105000-108123400	Weak transcription	Adipose Nuclei	Adipose
38	chr9:108105000-108124000	Weak transcription	Fetal Intestine Small	intestine
39	chr9:108105000-108125000	Weak transcription	HSMMtube	muscle
40	chr9:108105000-108129800	Weak transcription	Ovary	ovary
41	chr9:108105000-108133000	Weak transcription	Dnd41	blood
42	chr9:108105000-108133400	Weak transcription	Fetal Thymus	thymus
43	chr9:108105000-108149600	Weak transcription	Right Ventricle	heart
44	chr9:108105000-108151200	Weak transcription	Gastric	stomach
45	chr9:108105000-108154800	Weak transcription	Small Intestine	intestine
46	chr9:108105200-108149800	Weak transcription	NHDF-Ad	bronchial
47	chr9:108107000-108125200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:108107400-108120200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:108109000-108122400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr9:108109000-108123600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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