Variant report

Variant	rs7871668
Chromosome Location	chr9:27053650-27053651
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:27044880..27046633-chr9:27052693..27055070,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10738762	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs10757635	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10812488	0.83[JPT][hapmap]
rs10812503	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10812507	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10812508	0.85[ASN][1000 genomes]
rs10812509	0.80[JPT][hapmap]
rs10812510	0.81[JPT][hapmap]
rs10812515	0.83[ASN][1000 genomes]
rs10812517	0.81[JPT][hapmap]
rs10812518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10812519	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10812521	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10812523	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10812525	0.84[AMR][1000 genomes]
rs10967586	0.85[JPT][hapmap]
rs10967621	0.81[JPT][hapmap]
rs10967627	0.81[JPT][hapmap]
rs10967630	0.81[JPT][hapmap]
rs10967633	0.81[JPT][hapmap]
rs10967635	0.80[JPT][hapmap]
rs10967645	0.83[CHB][hapmap]
rs10967648	0.81[ASN][1000 genomes]
rs10967649	0.84[JPT][hapmap]
rs10967650	0.81[JPT][hapmap]
rs10967652	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10967670	0.83[ASN][1000 genomes]
rs10967678	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10967679	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10967680	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10967681	0.80[CHB][hapmap]
rs10967685	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10967688	0.80[CHB][hapmap];0.82[ASN][1000 genomes]
rs10967704	0.83[AMR][1000 genomes]
rs10967706	0.84[AMR][1000 genomes]
rs12337896	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs1541144	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1577328	0.89[CHB][hapmap]
rs1591355	0.83[AMR][1000 genomes]
rs17833941	0.81[JPT][hapmap]
rs1819539	0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2095405	0.88[AMR][1000 genomes]
rs2225720	0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs3739544	0.81[JPT][hapmap]
rs3758218	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4394491	0.83[AMR][1000 genomes]
rs4413873	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs4463511	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4621911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475945	0.95[JPT][hapmap]
rs6475954	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6475955	0.87[AMR][1000 genomes]
rs7018585	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7020010	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs7030567	0.87[AMR][1000 genomes]
rs7035447	0.80[JPT][hapmap]
rs7038218	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7040505	0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7042447	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7045747	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7849248	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7854191	0.92[ASN][1000 genomes]
rs7856462	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs7857447	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs7857669	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7859996	0.81[AMR][1000 genomes]
rs7860542	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7863476	0.94[JPT][hapmap]
rs7868158	0.94[JPT][hapmap]
rs7870787	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7872496	0.85[JPT][hapmap]
rs7874940	0.81[JPT][hapmap]
rs7875068	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7875171	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv466334	chr9:27028947-27098940	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv613944	chr9:27028947-27098940	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7871668	IFT74	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26985200-27063800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr9:26991800-27058000	Weak transcription	NHDF-Ad	bronchial
3	chr9:27009800-27070000	Weak transcription	Psoas Muscle	Psoas
4	chr9:27014400-27060800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:27014400-27068200	Weak transcription	Fetal Heart	heart
6	chr9:27018400-27065200	Weak transcription	Osteobl	bone
7	chr9:27019200-27061800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr9:27024400-27053800	Weak transcription	Lung	lung
9	chr9:27024400-27082600	Weak transcription	Gastric	stomach
10	chr9:27024600-27054400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:27024600-27056400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:27024600-27058800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr9:27024600-27059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:27024600-27061000	Weak transcription	Dnd41	blood
15	chr9:27024600-27061400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:27024600-27061800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:27024600-27064400	Weak transcription	Colonic Mucosa	Colon
18	chr9:27024600-27075800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:27024600-27078600	Weak transcription	Aorta	Aorta
20	chr9:27024600-27079000	Weak transcription	Pancreas	Pancrea
21	chr9:27024600-27082400	Weak transcription	Primary T cells from cord blood	blood
22	chr9:27024600-27083400	Weak transcription	Left Ventricle	heart
23	chr9:27024600-27085000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:27024600-27086800	Weak transcription	Right Ventricle	heart
25	chr9:27024800-27056800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:27024800-27058200	Weak transcription	Fetal Brain Male	brain
27	chr9:27024800-27060000	Weak transcription	Fetal Kidney	kidney
28	chr9:27024800-27094800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:27025200-27056000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:27025200-27064800	Weak transcription	Fetal Brain Female	brain
31	chr9:27025200-27078000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:27025400-27063600	Weak transcription	Brain Substantia Nigra	brain
33	chr9:27025400-27066800	Weak transcription	Brain Anterior Caudate	brain
34	chr9:27025400-27075600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:27036800-27054200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:27037000-27054200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:27037000-27069600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:27038000-27085000	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:27038200-27061000	Weak transcription	Fetal Intestine Large	intestine
40	chr9:27038200-27065400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr9:27042400-27058600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr9:27042400-27063600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:27045200-27054800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:27046000-27061000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:27046200-27058400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr9:27046600-27068000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:27047400-27058400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:27047600-27057400	Weak transcription	Brain Germinal Matrix	brain
49	chr9:27048800-27076200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr9:27049000-27065800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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