Variant report

Variant	rs10877888
Chromosome Location	chr12:62999154-62999155
allele	C/G
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	GATA3	chr12:62998469-62999219	SK-N-SH	brain:	n/a	chr12:62998843-62998851 chr12:62998844-62998851 chr12:62998842-62998855
2	POLR2A	chr12:62995037-63001628	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:62995668-63001032	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:62998610-62999256	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:62995938-63002376	U87	brain:	n/a	n/a
6	POLR2A	chr12:62995424-63002267	U87	brain:	n/a	n/a
7	POLR2A	chr12:62995938-63002365	U87	brain:	n/a	n/a
8	GATA3	chr12:62998390-62999296	MCF-7	breast:	n/a	chr12:62998843-62998851 chr12:62998844-62998851 chr12:62998842-62998855
9	GATA3	chr12:62998383-62999204	SK-N-SH	brain:	n/a	chr12:62998843-62998851 chr12:62998844-62998851 chr12:62998842-62998855
10	TCF12	chr12:62995491-63001122	A549	lung:	n/a	n/a
11	REST	chr12:62995795-62999212	H1-neurons	neurons:	n/a	chr12:62997605-62997615 chr12:62997314-62997327
12	POLR2A	chr12:62995454-63001211	HUVEC	blood vessel:	n/a	n/a
13	TBL1XR1	chr12:62998649-62999219	K562	blood:	n/a	n/a
14	POLR2A	chr12:62995424-63002364	U87	brain:	n/a	n/a
15	POLR2A	chr12:62995022-62999169	IMR90	lung:	n/a	n/a
16	GATA2	chr12:62998584-62999309	HUVEC	blood vessel:	n/a	chr12:62998844-62998851 chr12:62998842-62998855
17	CHD1	chr12:62995117-62999801	IMR90	lung:	n/a	n/a
18	CTCF	chr12:62999021-62999449	K562	blood:	n/a	n/a
19	POLR2A	chr12:62995208-63001924	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr12:62998759-63001578	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr12:62996032-63001077	A549	lung:	n/a	n/a
22	POLR2A	chr12:62995979-62999253	HUVEC	blood vessel:	n/a	n/a
23	SIN3AK20	chr12:62998436-62999251	MCF-7	breast:	n/a	n/a
24	POLR2A	chr12:62999080-62999608	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr12:62999024-63000915	PFSK-1	brain:	n/a	n/a
26	TCF7L2	chr12:62999141-62999364	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:62994755-63002267	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:62995027-62999211	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr12:62998470-62999276	A549	lung:	n/a	n/a
30	GATA3	chr12:62995840-63001125	A549	lung:	n/a	chr12:63001050-63001057 chr12:62998843-62998851 chr12:62998844-62998851 chr12:62997355-62997365 chr12:63001049-63001059 chr12:63001050-63001057 chr12:62998842-62998855 chr12:63001043-63001064 chr12:63001046-63001062 chr12:62999370-62999377 chr12:63001050-63001057
31	BCL3	chr12:62995675-63002413	A549	lung:	n/a	chr12:62997568-62997577 chr12:62997367-62997376
32	POLR2A	chr12:62995628-63002228	K562	blood:	n/a	n/a
33	POLR2A	chr12:62998677-62999202	GM12892	blood:	n/a	n/a
34	REST	chr12:62995843-63001063	A549	lung:	n/a	chr12:62997605-62997615 chr12:62997314-62997327

No.	Distal block	Cell Line	Cell type
1	chr12:62978077..62985603-chr12:62994484..62999339,10	MCF-7	breast:
2	chr12:62995008..63000778-chr12:63178750..63184772,7	MCF-7	breast:
3	chr12:62995127..63000683-chr12:63174450..63183073,15	MCF-7	breast:
4	chr12:62975073..62982220-chr12:62994233..63000379,9	K562	blood:
5	chr12:62998104..63000296-chr12:63188312..63190467,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MON2-2	chr12:62997216-63015942	NONHSAT029092
2	lnc-MON2-2	chr12:62999134-62999723	NONHSAT029094

Variant related genes	Relation type
C12orf61	TF binding region
ENSG00000061987	Chromatin interaction
ENSG00000111110	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10128830	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[MKK][hapmap];0.85[ASN][1000 genomes]
rs10128959	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10161549	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[MKK][hapmap];0.86[ASN][1000 genomes]
rs10219555	0.85[CHB][hapmap];0.87[MKK][hapmap]
rs10219765	0.95[CHB][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10784306	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs10784307	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10877866	0.91[CHB][hapmap]
rs10877872	0.86[CHB][hapmap]
rs10877873	0.90[CHB][hapmap]
rs10877876	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10877880	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10877883	0.81[CEU][hapmap];0.84[ASN][1000 genomes]
rs10877885	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[MKK][hapmap];0.86[ASN][1000 genomes]
rs10877886	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[MKK][hapmap];0.86[ASN][1000 genomes]
rs10877887	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877889	0.81[JPT][hapmap]
rs11174493	0.86[CHB][hapmap]
rs11174520	0.91[CHB][hapmap]
rs11174534	0.90[CHB][hapmap]
rs11174538	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs11174540	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs11174541	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs11174542	0.81[ASN][1000 genomes]
rs11174550	0.85[ASN][1000 genomes]
rs11174559	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11174572	0.80[JPT][hapmap]
rs11174573	0.81[JPT][hapmap]
rs12227568	0.81[ASN][1000 genomes]
rs12300696	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.84[ASN][1000 genomes]
rs12308140	0.83[MKK][hapmap]
rs12357	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12580048	0.86[ASN][1000 genomes]
rs12829103	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1498712	0.81[JPT][hapmap]
rs2047478	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2047479	0.81[ASN][1000 genomes]
rs4763021	0.85[CHB][hapmap]
rs4763174	0.91[CHB][hapmap]
rs4763177	0.88[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4763179	0.86[ASN][1000 genomes]
rs4763180	0.86[ASN][1000 genomes]
rs6581454	0.85[CHB][hapmap]
rs7136993	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7298782	0.91[CHB][hapmap]
rs7302027	0.90[CHB][hapmap]
rs7308021	0.81[CHB][hapmap]
rs7957417	0.90[CHB][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap]
rs7963657	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7968360	0.81[JPT][hapmap]
rs7975560	0.90[CHB][hapmap];0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62995200-62999600	Active TSS	Fetal Kidney	kidney
2	chr12:62995600-62999200	Active TSS	Stomach Smooth Muscle	stomach
3	chr12:62995800-62999200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:62995800-62999200	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr12:62995800-62999200	Active TSS	HSMM	muscle
6	chr12:62995800-62999400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:62995800-62999400	Active TSS	Fetal Stomach	stomach
8	chr12:62995800-62999600	Active TSS	Fetal Brain Male	brain
9	chr12:62995800-62999600	Active TSS	GM12878-XiMat	blood
10	chr12:62995800-62999600	Active TSS	NHLF	lung
11	chr12:62995800-62999800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:62995800-62999800	Active TSS	NHDF-Ad	bronchial
13	chr12:62996000-62999200	Active TSS	Aorta	Aorta
14	chr12:62996000-62999200	Active TSS	Fetal Intestine Large	intestine
15	chr12:62996000-62999200	Active TSS	Fetal Intestine Small	intestine
16	chr12:62996000-62999200	Active TSS	Fetal Muscle Trunk	muscle
17	chr12:62996000-62999200	Active TSS	Ovary	ovary
18	chr12:62996000-62999200	Active TSS	Psoas Muscle	Psoas
19	chr12:62996000-62999200	Active TSS	Right Ventricle	heart
20	chr12:62996000-62999400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:62996000-62999400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:62996000-62999400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:62996000-62999400	Active TSS	Muscle Satellite Cultured Cells	--
24	chr12:62996000-62999400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:62996000-62999600	Active TSS	HSMMtube	muscle
26	chr12:62996000-63000200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr12:62996000-63000400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:62996000-63000600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:62996200-62999200	Active TSS	NH-A	brain
30	chr12:62996200-62999400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr12:62996200-62999400	Active TSS	Fetal Muscle Leg	muscle
32	chr12:62996400-62999200	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr12:62997200-62999800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr12:62997600-63000200	Transcr. at gene 5' and 3'	A549	lung
35	chr12:62997800-62999200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr12:62997800-62999400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:62997800-63000000	Active TSS	Right Atrium	heart
38	chr12:62997800-63000400	Weak transcription	Esophagus	oesophagus
39	chr12:62997800-63000600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:62997800-63012800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:62997800-63019200	Weak transcription	Spleen	Spleen
42	chr12:62998000-62999600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr12:62998000-62999800	Enhancers	Stomach Mucosa	stomach
44	chr12:62998000-63000200	Transcr. at gene 5' and 3'	Osteobl	bone
45	chr12:62998000-63000400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:62998000-63010200	Weak transcription	Lung	lung
47	chr12:62998000-63019200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:62998200-62999200	Enhancers	Primary B cells from peripheral blood	blood
49	chr12:62998200-63001600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr12:62998400-62999200	Enhancers	Brain Substantia Nigra	brain

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