Variant report

Variant	rs2217938
Chromosome Location	chr3:51425674-51425675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:51424998-51425954	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:51425114-51425732	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:51425336-51426053	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr3:51424978-51426228	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:51424939-51428943	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:51424893-51425680	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:51420469-51426170	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:51424915-51429535	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:51424827-51426277	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51424798..51427104-chr3:51714699..51717497,2	MCF-7	breast:
2	chr3:50607017..50612379-chr3:51423330..51426962,5	MCF-7	breast:
3	chr3:51425475..51427809-chr3:51452594..51455305,2	MCF-7	breast:
4	chr3:50648976..50652431-chr3:51425600..51429805,4	K562	blood:
5	chr3:51425602..51427385-chr3:51461999..51464649,2	K562	blood:
6	chr3:50652955..50655582-chr3:51425473..51427383,2	MCF-7	breast:

No data

Variant related genes	Relation type
RBM15B	TF binding region
ENSG00000114738	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000164081	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10510757	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10510758	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485610	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12487426	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12487468	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12489219	0.83[CHD][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs12489414	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490471	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12490889	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12491048	0.98[ASN][1000 genomes]
rs12492624	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12493265	0.92[ASN][1000 genomes]
rs12493618	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493857	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12493978	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12494462	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12494979	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089799	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13090348	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370124	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051783	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051811	0.89[ASN][1000 genomes]
rs17661242	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17712228	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1842394	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2033703	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2061949	0.83[MEX][hapmap]
rs2082992	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2082993	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2101056	0.82[CHB][hapmap]
rs2170177	0.83[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs2241785	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304512	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306430	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306431	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2356261	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356298	0.94[ASN][1000 genomes]
rs35536327	0.89[ASN][1000 genomes]
rs3749317	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792408	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804766	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828395	0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4468966	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687553	0.90[ASN][1000 genomes]
rs4687563	0.91[ASN][1000 genomes]
rs4687601	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687605	0.94[ASN][1000 genomes]
rs4687610	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687656	0.93[ASN][1000 genomes]
rs4687691	0.91[ASN][1000 genomes]
rs4687731	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687777	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687794	0.91[ASN][1000 genomes]
rs4687803	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687804	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687811	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687812	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687813	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974096	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974098	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974112	0.83[CHD][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs55667499	0.92[ASN][1000 genomes]
rs55671465	0.85[ASN][1000 genomes]
rs56239081	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56729479	0.94[ASN][1000 genomes]
rs57027950	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57047724	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57603251	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57700326	0.87[ASN][1000 genomes]
rs57831708	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58059174	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58189274	0.82[ASN][1000 genomes]
rs58201844	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58568178	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58836277	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59563413	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59838596	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59953568	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60606339	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61233013	0.91[ASN][1000 genomes]
rs61419317	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61689323	0.92[ASN][1000 genomes]
rs72945708	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72945713	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72951443	0.92[ASN][1000 genomes]
rs73834252	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73834253	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73834254	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73834258	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73837436	0.94[AFR][1000 genomes]
rs73837439	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73837442	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837443	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751076	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630259	0.88[LWK][hapmap]
rs7635095	0.88[LWK][hapmap]
rs7642077	0.88[LWK][hapmap]
rs7642698	0.92[ASN][1000 genomes]
rs880478	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9817077	0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs9817872	0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs9819195	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9820140	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9827186	0.89[ASN][1000 genomes]
rs9829057	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs9842600	0.91[ASN][1000 genomes]
rs9843583	0.90[ASN][1000 genomes]
rs9856134	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9861019	0.86[ASN][1000 genomes]
rs9878592	0.83[CHD][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs9990213	0.81[LWK][hapmap]

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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51421400-51426000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:51423600-51426000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:51423600-51426000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
4	chr3:51423600-51427800	Genic enhancers	Primary T cells from cord blood	blood
5	chr3:51423800-51426000	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:51423800-51426000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:51423800-51426000	Enhancers	Fetal Brain Male	brain
8	chr3:51423800-51426000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
9	chr3:51423800-51426000	Transcr. at gene 5' and 3'	NHLF	lung
10	chr3:51423800-51426200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
11	chr3:51423800-51426600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:51423800-51427400	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr3:51423800-51428200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr3:51423800-51428400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:51424000-51426600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:51424000-51426600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:51424000-51426800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
18	chr3:51424000-51427400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:51424200-51425800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:51424200-51425800	Genic enhancers	Brain Anterior Caudate	brain
21	chr3:51424200-51426000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:51424200-51426200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:51424200-51428000	Genic enhancers	Fetal Intestine Large	intestine
24	chr3:51424200-51428000	Genic enhancers	Fetal Muscle Leg	muscle
25	chr3:51424400-51425800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:51424400-51425800	Active TSS	HSMMtube	muscle
27	chr3:51424400-51426000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:51424400-51426000	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:51424400-51426000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:51424400-51426200	Strong transcription	Rectal Smooth Muscle	rectum
31	chr3:51424400-51426400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:51424400-51426400	Genic enhancers	Fetal Lung	lung
33	chr3:51424400-51426400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:51424400-51427600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:51424400-51427800	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr3:51424400-51427800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:51424400-51428000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:51424400-51428000	Genic enhancers	Fetal Thymus	thymus
39	chr3:51424600-51426200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:51424600-51426200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:51424600-51426200	Genic enhancers	Esophagus	oesophagus
42	chr3:51424600-51426400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:51424600-51426400	Genic enhancers	Brain Hippocampus Middle	brain
44	chr3:51424600-51426400	Genic enhancers	Left Ventricle	heart
45	chr3:51424600-51426600	Strong transcription	Brain Cingulate Gyrus	brain
46	chr3:51424600-51426800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:51424600-51427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:51424600-51427400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:51424600-51427800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:51424600-51427800	Weak transcription	Psoas Muscle	Psoas

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