Variant report

Variant	rs235621
Chromosome Location	chr12:47055582-47055583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46972689..46974788-chr12:47053934..47056734,2	MCF-7	breast:
2	chr12:46747621..46748674-chr12:47054938..47055840,3	MCF-7	breast:
3	chr12:47054064..47055917-chr12:47057458..47059164,2	K562	blood:
4	chr12:46775880..46778772-chr12:47053263..47055840,3	MCF-7	breast:
5	chr12:46750763..46752796-chr12:47055390..47058156,2	MCF-7	breast:
6	chr12:46759450..46767729-chr12:47050364..47062392,28	MCF-7	breast:
7	chr12:46886016..46887722-chr12:47054283..47056459,2	MCF-7	breast:
8	chr12:46383988..46386138-chr12:47055082..47056612,2	MCF-7	breast:
9	chr12:46760654..46769647-chr12:47051646..47061944,32	MCF-7	breast:
10	chr12:46757823..46760512-chr12:47053505..47055776,2	K562	blood:
11	chr12:46775360..46780494-chr12:47054865..47060216,9	MCF-7	breast:
12	chr12:46887516..46889882-chr12:47054053..47056770,2	MCF-7	breast:
13	chr12:47053397..47056382-chr12:47060303..47062102,2	MCF-7	breast:
14	chr12:46762091..46766718-chr12:47051293..47055848,8	K562	blood:
15	chr12:46764217..46768302-chr12:47052891..47055832,5	K562	blood:
16	chr12:46776215..46777851-chr12:47053337..47055678,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139218	Chromatin interaction
ENSG00000258096	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10785631	1.00[CEU][hapmap]
rs10880975	1.00[CEU][hapmap]
rs10880976	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs10880977	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs11183497	1.00[CEU][hapmap]
rs11183524	0.90[EUR][1000 genomes]
rs11183536	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11183539	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11183547	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183550	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183610	0.81[MEX][hapmap]
rs11829502	1.00[CEU][hapmap]
rs11830099	0.84[EUR][1000 genomes]
rs11830501	0.84[EUR][1000 genomes]
rs11831177	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs11831920	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11831929	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11832316	0.84[EUR][1000 genomes]
rs11833393	0.90[EUR][1000 genomes]
rs11834607	0.90[EUR][1000 genomes]
rs11835517	0.84[EUR][1000 genomes]
rs11835974	0.84[EUR][1000 genomes]
rs11836915	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs11836940	1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs11837104	0.84[EUR][1000 genomes]
rs12300125	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12301825	0.81[MEX][hapmap]
rs12310635	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12320420	0.81[AMR][1000 genomes]
rs12578813	0.91[EUR][1000 genomes]
rs12579089	0.91[EUR][1000 genomes]
rs12579348	0.84[EUR][1000 genomes]
rs12579976	0.84[EUR][1000 genomes]
rs12580092	0.91[EUR][1000 genomes]
rs12580121	1.00[CEU][hapmap]
rs12580356	0.91[EUR][1000 genomes]
rs12580488	0.95[EUR][1000 genomes]
rs12581205	0.89[EUR][1000 genomes]
rs12581311	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12581366	0.91[EUR][1000 genomes]
rs12582013	0.95[EUR][1000 genomes]
rs12582056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582305	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs12582476	0.91[EUR][1000 genomes]
rs17096991	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17096995	1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs17097002	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17097009	0.84[EUR][1000 genomes]
rs17097022	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[EUR][1000 genomes]
rs17097246	0.82[MEX][hapmap]
rs17121410	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17121412	1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs17594275	0.95[EUR][1000 genomes]
rs17611638	0.91[EUR][1000 genomes]
rs180431	0.82[MEX][hapmap]
rs1946175	0.90[EUR][1000 genomes]
rs2042058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2193662	0.81[EUR][1000 genomes]
rs2193663	0.84[EUR][1000 genomes]
rs2216439	0.81[EUR][1000 genomes]
rs235600	0.91[AMR][1000 genomes]
rs235601	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs235602	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs235607	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs235610	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs235616	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs235617	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs235622	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs235625	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs235626	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs235627	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408576	0.84[EUR][1000 genomes]
rs2408577	0.90[EUR][1000 genomes]
rs2430937	0.90[EUR][1000 genomes]
rs2430939	0.90[EUR][1000 genomes]
rs2430940	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2430941	0.90[EUR][1000 genomes]
rs2430942	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2430943	0.90[EUR][1000 genomes]
rs2430946	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2430947	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2471583	1.00[CEU][hapmap]
rs2471588	0.90[EUR][1000 genomes]
rs2471594	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2471601	0.90[EUR][1000 genomes]
rs2471602	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2471605	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2471608	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2471617	0.90[EUR][1000 genomes]
rs2471618	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs28768973	0.90[EUR][1000 genomes]
rs2897969	0.81[EUR][1000 genomes]
rs2909411	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2960450	0.90[EUR][1000 genomes]
rs34008890	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35096979	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4604970	0.84[EUR][1000 genomes]
rs4768125	0.83[EUR][1000 genomes]
rs4768740	0.91[MEX][hapmap]
rs4768741	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768742	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768744	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56111534	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56152575	0.84[EUR][1000 genomes]
rs56181923	0.84[EUR][1000 genomes]
rs56271434	0.84[EUR][1000 genomes]
rs57370043	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57658610	0.90[EUR][1000 genomes]
rs58449317	0.84[EUR][1000 genomes]
rs58503088	0.84[EUR][1000 genomes]
rs58561072	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58813899	0.84[EUR][1000 genomes]
rs59903937	0.84[EUR][1000 genomes]
rs60191997	0.90[EUR][1000 genomes]
rs60669661	0.84[EUR][1000 genomes]
rs60681792	0.84[EUR][1000 genomes]
rs61072098	0.86[EUR][1000 genomes]
rs61355826	0.90[EUR][1000 genomes]
rs61641663	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6582666	1.00[CEU][hapmap]
rs7138914	0.84[EUR][1000 genomes]
rs7295471	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs7308386	0.84[EUR][1000 genomes]
rs7310326	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7310408	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7310614	0.91[MEX][hapmap]
rs73282109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73290402	0.84[EUR][1000 genomes]
rs73291964	0.84[EUR][1000 genomes]
rs73291976	0.84[EUR][1000 genomes]
rs73291980	0.84[EUR][1000 genomes]
rs73292000	0.84[EUR][1000 genomes]
rs73292001	0.90[EUR][1000 genomes]
rs73293911	0.84[EUR][1000 genomes]
rs73293919	0.84[EUR][1000 genomes]
rs7484802	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7488464	0.90[EUR][1000 genomes]
rs765707	0.84[EUR][1000 genomes]
rs766794	0.91[EUR][1000 genomes]
rs7976710	0.84[EUR][1000 genomes]
rs9669050	0.90[EUR][1000 genomes]
rs977069	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558783	chr12:46996632-47144856	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1844378	chr12:47028797-47072016	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47046400-47069800	Weak transcription	Pancreas	Pancrea
2	chr12:47046800-47057000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:47050800-47056000	Enhancers	NHLF	lung
4	chr12:47051000-47056200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:47051400-47055600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr12:47051400-47055800	Enhancers	Fetal Heart	heart
7	chr12:47051400-47055800	Enhancers	HSMM	muscle
8	chr12:47051400-47056200	Enhancers	HUVEC	blood vessel
9	chr12:47051400-47059800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:47051600-47055600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr12:47051800-47056000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr12:47051800-47056000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:47052200-47055600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr12:47052400-47055600	Enhancers	Primary T cells from cord blood	blood
15	chr12:47052600-47056000	Enhancers	Primary hematopoietic stem cells	blood
16	chr12:47053000-47055800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:47053200-47055600	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:47053200-47055800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:47053400-47055600	Enhancers	Fetal Lung	lung
20	chr12:47053400-47055800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr12:47053400-47058200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr12:47053400-47058600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:47053400-47062400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:47053600-47055600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr12:47053600-47055600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:47053600-47055800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:47053600-47056000	Enhancers	NH-A	brain
28	chr12:47053600-47056200	Enhancers	HMEC	breast
29	chr12:47053800-47055600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr12:47053800-47058800	Enhancers	Hela-S3	cervix
31	chr12:47054000-47055800	Enhancers	Dnd41	blood
32	chr12:47054000-47068400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:47054000-47071400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:47054200-47055600	Enhancers	Fetal Kidney	kidney
35	chr12:47054200-47055600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr12:47054400-47055800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:47054400-47056000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:47054400-47056000	Enhancers	HepG2	liver
39	chr12:47054400-47057000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:47054400-47059400	Weak transcription	Psoas Muscle	Psoas
41	chr12:47054600-47055600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr12:47054600-47055600	Enhancers	K562	blood
43	chr12:47054600-47058200	Enhancers	NHEK	skin
44	chr12:47054800-47055800	Enhancers	HSMMtube	muscle
45	chr12:47054800-47058200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:47055000-47055600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr12:47055000-47055600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:47055000-47056000	Enhancers	Osteobl	bone
49	chr12:47055000-47058600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:47055200-47055600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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