Variant report

Variant	rs295443
Chromosome Location	chr3:47337701-47337702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47337672..47341036-chr3:47345432..47347929,3	K562	blood:
2	chr3:47330452..47333849-chr3:47334869..47338744,4	MCF-7	breast:
3	chr3:47323372..47326366-chr3:47337032..47339146,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114648	Chromatin interaction
ENSG00000088727	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1024036	0.83[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1038393	1.00[EUR][1000 genomes]
rs10865945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865947	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs1091068	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11130122	0.87[AMR][1000 genomes]
rs11707272	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	1.00[EUR][1000 genomes]
rs11709693	1.00[EUR][1000 genomes]
rs11922925	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12330516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12491029	1.00[YRI][hapmap]
rs12631697	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13077134	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs13078181	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13079174	0.87[AMR][1000 genomes]
rs13084060	1.00[AMR][1000 genomes]
rs13323092	0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531874	0.91[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs1638677	0.84[AFR][1000 genomes]
rs1872165	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs1874264	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2350642	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28735306	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295431	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	0.91[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295444	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295445	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295448	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.82[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	0.91[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.82[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4018904	0.82[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs448018	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4858812	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs4858823	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442066	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6442068	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs648226	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6772449	0.82[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6778673	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778687	0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6780994	1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	1.00[EUR][1000 genomes]
rs6787210	0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6788978	1.00[EUR][1000 genomes]
rs6789730	1.00[EUR][1000 genomes]
rs6808117	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7372780	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs73831482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630154	0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7639121	0.82[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643150	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643181	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7644043	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7644382	0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	0.82[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807930	0.91[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900688	1.00[EUR][1000 genomes]
rs900689	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs900690	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	1.00[EUR][1000 genomes]
rs900693	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs900694	0.91[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs903538	0.91[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs924009	0.89[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936186	1.00[EUR][1000 genomes]
rs9812407	1.00[EUR][1000 genomes]
rs9819475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9823480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9826488	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9827293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828124	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9828289	0.84[AFR][1000 genomes]
rs9828473	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861247	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9862711	1.00[EUR][1000 genomes]
rs9869489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878813	1.00[EUR][1000 genomes]
rs9883152	1.00[EUR][1000 genomes]
rs9990284	1.00[EUR][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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47325400-47361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:47325600-47337800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:47325600-47338000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:47325600-47344600	Weak transcription	Ovary	ovary
5	chr3:47325600-47367600	Weak transcription	A549	lung
6	chr3:47325800-47338000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:47325800-47338200	Weak transcription	HUVEC	blood vessel
8	chr3:47325800-47343800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:47325800-47352000	Weak transcription	Fetal Kidney	kidney
10	chr3:47326200-47340800	Weak transcription	Fetal Intestine Large	intestine
11	chr3:47326200-47344600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:47326200-47356200	Weak transcription	Fetal Heart	heart
13	chr3:47326200-47356600	Weak transcription	NHDF-Ad	bronchial
14	chr3:47326200-47359600	Weak transcription	Fetal Lung	lung
15	chr3:47326200-47362200	Weak transcription	Gastric	stomach
16	chr3:47326200-47363200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:47326400-47338200	Weak transcription	Stomach Mucosa	stomach
18	chr3:47326400-47364400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:47326600-47341200	Weak transcription	Placenta	Placenta
20	chr3:47326600-47351600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:47326800-47356600	Weak transcription	Small Intestine	intestine
22	chr3:47327000-47344400	Weak transcription	Brain Angular Gyrus	brain
23	chr3:47327600-47348400	Weak transcription	Fetal Brain Male	brain
24	chr3:47328400-47364400	Weak transcription	Pancreas	Pancrea
25	chr3:47328600-47338400	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:47329200-47359800	Weak transcription	NHLF	lung
27	chr3:47329600-47340800	Weak transcription	Fetal Intestine Small	intestine
28	chr3:47330000-47343400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:47330400-47352000	Weak transcription	NHEK	skin
30	chr3:47330400-47356000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:47330600-47346200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:47330600-47359800	Weak transcription	Hela-S3	cervix
33	chr3:47330600-47360600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:47330800-47344200	Weak transcription	HSMMtube	muscle
35	chr3:47330800-47356600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:47330800-47361800	Weak transcription	HMEC	breast
37	chr3:47331000-47344000	Weak transcription	HSMM	muscle
38	chr3:47331200-47344000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:47331400-47337800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:47331400-47343200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:47331400-47343400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:47331800-47338000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:47332200-47338000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:47332200-47361800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:47332400-47340000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:47332400-47355600	Weak transcription	Brain Substantia Nigra	brain
47	chr3:47332600-47338000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:47332600-47338600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:47332600-47343000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:47332600-47343400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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