Variant report

Variant	rs9855171
Chromosome Location	chr3:159488492-159488493
allele	G/T
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	USF2	chr3:159488335-159488526	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:159488439-159488513	ProgFib	skin:	n/a	n/a
3	FOXA1	chr3:159488251-159488619	T-47D	breast:	n/a	n/a
4	FOXA1	chr3:159488226-159488583	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159480986..159483259-chr3:159486958..159490196,4	MCF-7	breast:
2	chr3:159487312..159489793-chr3:159503414..159505696,2	MCF-7	breast:

Variant related genes	Relation type
IQCJ-SCHIP1-AS1	TF binding region
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10440023	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470474	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470475	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10513545	1.00[TSI][hapmap]
rs13314923	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28695486	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4621369	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56786891	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6781743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015941	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015967	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017937	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017943	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017960	1.00[EUR][1000 genomes]
rs7612849	1.00[EUR][1000 genomes]
rs7615917	0.83[AMR][1000 genomes]
rs7651449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9811600	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814058	1.00[EUR][1000 genomes]
rs9816506	1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs9830331	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9832139	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9845205	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845849	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846391	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846673	1.00[TSI][hapmap]
rs9846819	1.00[EUR][1000 genomes]
rs9850723	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][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]
rs9853947	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853973	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861347	1.00[TSI][hapmap]
rs9872127	0.83[AMR][1000 genomes]
rs9877761	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878860	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9880866	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159483600-159493000	Weak transcription	Gastric	stomach
2	chr3:159483800-159493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:159484000-159494600	Weak transcription	Psoas Muscle	Psoas
4	chr3:159484200-159493200	Weak transcription	Lung	lung
5	chr3:159484200-159501200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:159484400-159493000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:159484400-159493000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:159484400-159493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:159484400-159493200	Weak transcription	Fetal Stomach	stomach
10	chr3:159484400-159505400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:159484600-159500400	Weak transcription	Fetal Intestine Small	intestine
12	chr3:159484800-159489800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:159484800-159493000	Weak transcription	HSMMtube	muscle
14	chr3:159485000-159492600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:159485000-159492800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:159485000-159493000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:159485600-159489600	Weak transcription	Aorta	Aorta
18	chr3:159485600-159493000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:159485600-159493000	Weak transcription	HMEC	breast
20	chr3:159485600-159493400	Weak transcription	Fetal Brain Female	brain
21	chr3:159485800-159489000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:159485800-159493000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:159486200-159489000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:159486200-159492200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:159486400-159491000	Weak transcription	HUVEC	blood vessel
26	chr3:159486600-159488800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:159486600-159489600	Weak transcription	HSMM	muscle
28	chr3:159486600-159493200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:159486800-159488800	Weak transcription	NHDF-Ad	bronchial
30	chr3:159486800-159489600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:159486800-159489800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:159486800-159489800	Weak transcription	Left Ventricle	heart
33	chr3:159486800-159493000	Weak transcription	Right Ventricle	heart
34	chr3:159486800-159493000	Weak transcription	NH-A	brain
35	chr3:159486800-159493000	Weak transcription	NHEK	skin
36	chr3:159486800-159494000	Weak transcription	Fetal Heart	heart
37	chr3:159487000-159488600	Weak transcription	NHLF	lung
38	chr3:159487000-159489600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:159487000-159490400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:159487600-159488600	Enhancers	Brain Angular Gyrus	brain
41	chr3:159487600-159489400	Enhancers	Colon Smooth Muscle	Colon
42	chr3:159487600-159489800	Enhancers	Brain Substantia Nigra	brain
43	chr3:159487600-159493000	Weak transcription	Right Atrium	heart
44	chr3:159487800-159489000	Enhancers	Brain Hippocampus Middle	brain
45	chr3:159487800-159489400	Enhancers	Brain Cingulate Gyrus	brain
46	chr3:159488000-159488600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr3:159488000-159488600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr3:159488000-159489200	Enhancers	Stomach Smooth Muscle	stomach
49	chr3:159488200-159488600	Enhancers	Brain Anterior Caudate	brain
50	chr3:159488200-159488600	Enhancers	Pancreas	Pancrea

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