Variant report

Variant	rs12337896
Chromosome Location	chr9:27018020-27018021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10738762	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs10757635	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs10757636	0.92[AMR][1000 genomes]
rs10812488	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs10812503	0.88[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10812504	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10812507	0.88[CHB][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10812508	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10812513	0.81[ASN][1000 genomes]
rs10812515	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10812516	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10812518	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10812519	0.82[ASN][1000 genomes]
rs10812521	0.86[ASN][1000 genomes]
rs10967635	0.88[CHD][hapmap]
rs10967645	0.82[CHB][hapmap]
rs10967649	0.91[CHD][hapmap]
rs10967652	0.83[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10967661	0.85[CHD][hapmap]
rs10967666	0.81[ASN][1000 genomes]
rs10967668	0.80[ASN][1000 genomes]
rs10967670	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10967679	0.83[CEU][hapmap];0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs10967680	0.83[ASN][1000 genomes]
rs11534185	0.80[ASN][1000 genomes]
rs12236850	0.88[CHD][hapmap]
rs1541144	0.89[CHB][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1577328	0.81[JPT][hapmap]
rs1819539	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2225720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3739547	0.91[CHD][hapmap]
rs3758218	0.94[ASW][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4413873	0.82[CHB][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4621911	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs6475954	0.83[CEU][hapmap];0.89[CHB][hapmap]
rs7018585	0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7020010	0.89[CHB][hapmap]
rs7032756	0.83[ASW][hapmap]
rs7034478	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7034670	0.81[AMR][1000 genomes]
rs7035447	0.88[CHD][hapmap]
rs7038218	0.83[CHB][hapmap]
rs7040505	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7042447	0.83[CHB][hapmap]
rs7045747	0.82[ASN][1000 genomes]
rs7849248	0.88[CHB][hapmap];0.97[CHD][hapmap]
rs7854191	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7856462	0.82[CHB][hapmap]
rs7857669	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.85[ASN][1000 genomes]
rs7860542	0.83[CHB][hapmap]
rs7863476	0.88[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.82[AMR][1000 genomes]
rs7868158	1.00[MEX][hapmap]
rs7870787	0.83[CHB][hapmap]
rs7871668	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs7873073	0.90[CHD][hapmap]
rs7875068	0.89[CHB][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9644870	0.91[CHD][hapmap]

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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12337896	IFT74	cis	lymphoblastoid	seeQTL
rs12337896	IFT74	cis	parietal	SCAN
rs12337896	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957000-27024000	Weak transcription	Esophagus	oesophagus
2	chr9:26957200-27026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:26974200-27023600	Weak transcription	Fetal Brain Female	brain
5	chr9:26977200-27019400	Weak transcription	NH-A	brain
6	chr9:26977800-27026000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:26979400-27024000	Weak transcription	Small Intestine	intestine
8	chr9:26982800-27023800	Weak transcription	Lung	lung
9	chr9:26983600-27023800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:26985200-27024000	Weak transcription	Right Ventricle	heart
11	chr9:26985200-27024000	Weak transcription	HSMM	muscle
12	chr9:26985200-27063800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:26985400-27024000	Weak transcription	A549	lung
14	chr9:26985600-27024400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:26985800-27018800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:26987200-27023800	Weak transcription	HSMMtube	muscle
17	chr9:26987400-27019000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:26987400-27024000	Weak transcription	Aorta	Aorta
19	chr9:26991800-27058000	Weak transcription	NHDF-Ad	bronchial
20	chr9:27004000-27023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr9:27005200-27024000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:27005800-27024000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:27006400-27024000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:27006600-27023800	Weak transcription	Colonic Mucosa	Colon
25	chr9:27006600-27024200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:27008600-27022000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:27008600-27023800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:27009200-27019000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr9:27009400-27023800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:27009800-27023800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr9:27009800-27070000	Weak transcription	Psoas Muscle	Psoas
32	chr9:27010600-27023800	Weak transcription	Thymus	Thymus
33	chr9:27010600-27024000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:27010800-27023800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:27011000-27024200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:27011200-27023800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:27011200-27037400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr9:27011600-27026400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:27012000-27019400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:27012000-27021400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:27012000-27022600	Strong transcription	Fetal Lung	lung
42	chr9:27012000-27048800	Weak transcription	HepG2	liver
43	chr9:27012600-27019000	Weak transcription	Fetal Intestine Small	intestine
44	chr9:27012600-27026200	Weak transcription	Placenta	Placenta
45	chr9:27012800-27019000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:27013000-27018800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:27013000-27024000	Weak transcription	Fetal Brain Male	brain
48	chr9:27013200-27025400	Weak transcription	HUVEC	blood vessel
49	chr9:27013600-27023800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr9:27013600-27024000	Weak transcription	Brain Anterior Caudate	brain

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