Variant report

Variant	rs2239201
Chromosome Location	chr12:120538952-120538953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr12:120538690-120539656	GM12878	blood:	n/a	n/a
2	MTA3	chr12:120538856-120539519	GM12878	blood:	n/a	n/a
3	STAT5A	chr12:120538916-120539463	GM12878	blood:	n/a	chr12:120539307-120539318
4	USF1	chr12:120538875-120539223	SK-N-SH_RA	brain:	n/a	n/a
5	MXI1	chr12:120538037-120538952	IMR90	lung:	n/a	n/a
6	USF1	chr12:120538882-120539250	SK-N-SH_RA	brain:	n/a	n/a
7	USF1	chr12:120538869-120539304	SK-N-SH	brain:	n/a	n/a
8	MXI1	chr12:120538132-120539565	SK-N-SH	brain:	n/a	chr12:120539535-120539544

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:120537048..120541245-chr12:120553607..120557723,6	MCF-7	breast:
2	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
3	chr12:120538101..120541195-chr12:120726908..120731130,5	MCF-7	breast:
4	chr12:120534104..120540073-chr12:120552292..120555790,7	K562	blood:
5	chr12:120538883..120540818-chr12:120636912..120639321,2	MCF-7	breast:
6	chr12:120515805..120518721-chr12:120536191..120539691,3	MCF-7	breast:

No data

Variant related genes	Relation type
RAB35	TF binding region
ENSG00000200795	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10128766	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs10400498	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10400560	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849731	0.86[ASN][1000 genomes]
rs10849732	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10849735	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10849736	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.92[ASN][1000 genomes]
rs11064987	0.84[ASN][1000 genomes]
rs11064988	0.85[ASN][1000 genomes]
rs11064996	0.87[ASN][1000 genomes]
rs11065003	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.92[ASN][1000 genomes]
rs11833221	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12310269	0.87[ASN][1000 genomes]
rs12310591	0.92[ASN][1000 genomes]
rs12313413	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12318774	0.86[ASN][1000 genomes]
rs12320793	0.84[ASN][1000 genomes]
rs12322236	0.86[ASN][1000 genomes]
rs12422923	0.92[ASN][1000 genomes]
rs16949901	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16949946	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16949961	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17841967	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239200	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];0.94[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]
rs2239202	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239204	0.99[ASN][1000 genomes]
rs2240311	0.87[CHB][hapmap]
rs2283359	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283360	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283361	0.82[ASN][1000 genomes]
rs2286040	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28726166	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3852586	0.83[CHB][hapmap]
rs4767869	0.86[ASN][1000 genomes]
rs4767871	0.92[ASN][1000 genomes]
rs4767872	0.92[ASN][1000 genomes]
rs4767875	0.92[ASN][1000 genomes]
rs4767876	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58272825	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59168361	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60466490	0.92[ASN][1000 genomes]
rs6490281	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs6490284	0.83[CHB][hapmap]
rs7298183	0.86[ASN][1000 genomes]
rs7298727	0.86[ASN][1000 genomes]
rs7300023	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7306739	0.83[CHB][hapmap]
rs7312971	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7397339	0.92[ASN][1000 genomes]
rs7958402	0.86[ASN][1000 genomes]
rs7958497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs7965829	0.86[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7968557	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978927	0.91[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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv560434	chr12:120534147-120545718	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120525600-120539200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:120525600-120551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:120525800-120539200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:120525800-120553400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:120527400-120546800	Strong transcription	Thymus	Thymus
6	chr12:120527600-120539200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:120527600-120539800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:120527600-120540400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:120527600-120546000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:120529000-120540400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:120529000-120546800	Strong transcription	Dnd41	blood
12	chr12:120529600-120543000	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:120529800-120539200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:120529800-120542200	Strong transcription	Fetal Intestine Large	intestine
15	chr12:120530000-120539200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr12:120530800-120540400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:120532200-120539000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:120532200-120539600	Strong transcription	Primary T cells from cord blood	blood
19	chr12:120532400-120539000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr12:120532400-120539800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr12:120532600-120539000	Strong transcription	GM12878-XiMat	blood
22	chr12:120532600-120539200	Strong transcription	Fetal Intestine Small	intestine
23	chr12:120532600-120539400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:120532600-120539400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:120532600-120539600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:120532800-120541600	Weak transcription	K562	blood
27	chr12:120533600-120542800	Strong transcription	A549	lung
28	chr12:120533800-120553000	Weak transcription	Fetal Kidney	kidney
29	chr12:120534000-120539200	Strong transcription	Liver	Liver
30	chr12:120534200-120539200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:120534200-120542800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:120534200-120542800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:120534200-120542800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:120534400-120553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:120534600-120546800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:120534600-120547200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:120534600-120548200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:120534800-120539600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:120536000-120541800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr12:120536200-120543000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:120536600-120539000	Strong transcription	Primary B cells from cord blood	blood
42	chr12:120536800-120540800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:120536800-120541200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:120536800-120541800	Genic enhancers	Esophagus	oesophagus
45	chr12:120537000-120539400	Weak transcription	Small Intestine	intestine
46	chr12:120537000-120540800	Genic enhancers	Right Ventricle	heart
47	chr12:120537000-120540800	Weak transcription	Hela-S3	cervix
48	chr12:120537000-120543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:120537200-120539200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:120537200-120541000	Weak transcription	H9 Cell Line	embryonic stem cell

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