Variant report

Variant	rs1410839
Chromosome Location	chr9:108147078-108147079
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	IRF1	chr9:108146940-108148188	K562	blood:	n/a	chr9:108147825-108147839 chr9:108147825-108147835 chr9:108147819-108147829 chr9:108147823-108147837 chr9:108148076-108148089 chr9:108147819-108147833 chr9:108147821-108147835 chr9:108147817-108147837 chr9:108147819-108147840 chr9:108147823-108147834 chr9:108147817-108147831 chr9:108147818-108147831 chr9:108148146-108148157 chr9:108147818-108147831 chr9:108147827-108147836

Variant related genes	Relation type
SLC44A1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10123494	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10491810	1.00[ASN][1000 genomes]
rs10820801	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10991629	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]
rs10991639	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]
rs12339823	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12340765	1.00[ASN][1000 genomes]
rs12342542	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12344130	0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs12350138	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs13294525	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13294539	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410837	1.00[ASN][1000 genomes]
rs1553870	1.00[ASN][1000 genomes]
rs1553873	1.00[ASN][1000 genomes]
rs16924529	1.00[ASN][1000 genomes]
rs16924530	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.88[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];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2771031	1.00[ASN][1000 genomes]
rs2771033	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2771040	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812314	1.00[ASN][1000 genomes]
rs2812316	1.00[ASN][1000 genomes]
rs3199966	1.00[ASW][hapmap];0.85[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34750132	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35603631	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296093	1.00[ASN][1000 genomes]
rs4549843	0.84[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479311	1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479313	0.92[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479314	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479315	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479316	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7024985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029443	1.00[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7045091	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.92[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7873937	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs907230	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs1410839	ZNF189	cis	cerebellum	SCAN
rs1410839	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL
rs1410839	CYLC2	cis	parietal	SCAN
rs1410839	OR13F1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:108092000-108148000	Weak transcription	Psoas Muscle	Psoas
4	chr9:108093200-108149800	Weak transcription	HUVEC	blood vessel
5	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:108100200-108149600	Weak transcription	Pancreas	Pancrea
7	chr9:108104800-108147600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:108105000-108149600	Weak transcription	Right Ventricle	heart
9	chr9:108105000-108151200	Weak transcription	Gastric	stomach
10	chr9:108105000-108154800	Weak transcription	Small Intestine	intestine
11	chr9:108105200-108149800	Weak transcription	NHDF-Ad	bronchial
12	chr9:108117400-108147400	Weak transcription	Spleen	Spleen
13	chr9:108118200-108147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:108118600-108147600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr9:108121600-108157000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:108121800-108148600	Weak transcription	A549	lung
17	chr9:108122400-108148200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:108122600-108153400	Weak transcription	Stomach Mucosa	stomach
19	chr9:108123600-108154400	Weak transcription	Colonic Mucosa	Colon
20	chr9:108123800-108147600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:108124200-108147600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:108124400-108147400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr9:108124400-108151000	Weak transcription	Fetal Brain Male	brain
24	chr9:108124600-108151800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:108125000-108166800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr9:108125400-108147600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:108125400-108149800	Weak transcription	HSMMtube	muscle
28	chr9:108125600-108157000	Weak transcription	Osteobl	bone
29	chr9:108126000-108152000	Weak transcription	Brain Germinal Matrix	brain
30	chr9:108126400-108147800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:108127000-108147800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr9:108127200-108151800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:108128200-108151400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr9:108130200-108147800	Weak transcription	Ovary	ovary
35	chr9:108130800-108147600	Weak transcription	Primary B cells from cord blood	blood
36	chr9:108135000-108147600	Weak transcription	Thymus	Thymus
37	chr9:108136200-108152000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:108137000-108147400	Weak transcription	Primary T cells from cord blood	blood
39	chr9:108137400-108150600	Weak transcription	Fetal Heart	heart
40	chr9:108137800-108147200	Weak transcription	Colon Smooth Muscle	Colon
41	chr9:108137800-108147600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:108137800-108147600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr9:108137800-108147600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr9:108137800-108147600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr9:108137800-108147600	Weak transcription	Fetal Thymus	thymus
46	chr9:108137800-108147600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr9:108137800-108147600	Weak transcription	HSMM	muscle
48	chr9:108137800-108147800	Weak transcription	Fetal Muscle Leg	muscle
49	chr9:108137800-108155400	Weak transcription	Lung	lung
50	chr9:108137800-108156200	Weak transcription	Fetal Stomach	stomach

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