Variant report

Variant	rs7871097
Chromosome Location	chr9:26917691-26917692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:26916453..26918624-chr9:26922589..26924975,2	MCF-7	breast:
2	chr9:26916059..26918354-chr9:26923172..26926170,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137055	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10283643	1.00[CHB][hapmap]
rs10511793	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10738762	0.82[TSI][hapmap]
rs10757635	0.82[TSI][hapmap]
rs10812492	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10812500	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967593	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10967594	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967624	1.00[CHB][hapmap]
rs10967625	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs10967634	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10967639	1.00[CHB][hapmap]
rs10967640	1.00[CHB][hapmap]
rs1161603	1.00[CHB][hapmap]
rs12001845	1.00[CHB][hapmap]
rs12002260	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003612	1.00[CHD][hapmap]
rs12004732	0.80[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12338678	1.00[CHB][hapmap]
rs12342005	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345094	1.00[CHB][hapmap]
rs12349359	1.00[CHB][hapmap]
rs12352441	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs16910888	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910895	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694121	1.00[CHB][hapmap]
rs17694140	1.00[CHB][hapmap]
rs17694300	1.00[CHB][hapmap]
rs17694306	1.00[CHB][hapmap]
rs17694549	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17755887	1.00[CHB][hapmap]
rs17755911	1.00[CHB][hapmap]
rs2152063	1.00[CHB][hapmap]
rs2991949	1.00[CHB][hapmap]
rs3429	1.00[CHB][hapmap]
rs596427	1.00[CHB][hapmap]
rs615532	1.00[CHB][hapmap]
rs62542667	0.86[ASN][1000 genomes]
rs62544439	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544444	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6475948	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019692	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7024415	0.86[EUR][1000 genomes]
rs7032756	0.84[TSI][hapmap]
rs7035755	0.90[GIH][hapmap]
rs7037860	1.00[CHB][hapmap]
rs7038218	0.81[CEU][hapmap]
rs7039400	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7040516	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045881	0.96[GIH][hapmap];0.89[MEX][hapmap]
rs73436047	0.86[ASN][1000 genomes]
rs7851582	1.00[ASN][1000 genomes]
rs7863476	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs7868158	0.88[TSI][hapmap]
rs7871286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7871097	IFT74	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26893000-26922600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:26893000-26924200	Weak transcription	Esophagus	oesophagus
3	chr9:26893200-26923200	Weak transcription	Right Ventricle	heart
4	chr9:26893400-26925000	Weak transcription	Stomach Mucosa	stomach
5	chr9:26893400-26936400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:26893400-26936400	Weak transcription	Psoas Muscle	Psoas
7	chr9:26898200-26924400	Weak transcription	Aorta	Aorta
8	chr9:26899200-26921200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:26900800-26930000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:26901200-26935800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:26901600-26920800	Weak transcription	Gastric	stomach
12	chr9:26902800-26936600	Weak transcription	Spleen	Spleen
13	chr9:26903000-26927800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:26903000-26929800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:26903000-26935200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr9:26903200-26928400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:26903200-26930000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:26903200-26932600	Strong transcription	Dnd41	blood
19	chr9:26903200-26935200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr9:26903800-26927800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:26903800-26931600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:26904600-26935200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:26905400-26938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:26905800-26937400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr9:26906000-26921200	Weak transcription	Fetal Brain Male	brain
26	chr9:26906200-26928800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:26906200-26936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr9:26909200-26925200	Weak transcription	K562	blood
29	chr9:26911200-26926000	Strong transcription	Primary T cells from cord blood	blood
30	chr9:26911600-26930000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:26911600-26930000	Strong transcription	Placenta	Placenta
32	chr9:26912000-26928600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr9:26912000-26932600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr9:26912800-26928000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr9:26912800-26935000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:26913200-26928400	Strong transcription	NH-A	brain
37	chr9:26913200-26932600	Strong transcription	Primary B cells from cord blood	blood
38	chr9:26913400-26928000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:26913600-26927400	Strong transcription	Fetal Thymus	thymus
40	chr9:26913600-26928000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr9:26913600-26928600	Strong transcription	GM12878-XiMat	blood
42	chr9:26913800-26921000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:26914200-26928800	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr9:26914600-26930000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:26914600-26935600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:26914800-26921800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr9:26915000-26926800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr9:26915000-26927000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr9:26915000-26928600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr9:26915200-26918200	Strong transcription	Brain Cingulate Gyrus	brain

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