Variant report

Variant	rs6488079
Chromosome Location	chr12:9804215-9804216
allele	C/T
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	POLR2A	chr12:9799451-9804403	GM19193	blood:	n/a	n/a
2	MAX	chr12:9803994-9804287	K562	blood:	n/a	n/a
3	SPI1	chr12:9803915-9804357	HL-60	blood:	n/a	n/a
4	MTA3	chr12:9799406-9804477	GM12878	blood:	n/a	n/a
5	TBP	chr12:9803954-9804332	K562	blood:	n/a	n/a
6	MYC	chr12:9802783-9804371	NB4	blood:	n/a	chr12:9803552-9803562
7	MAX	chr12:9802772-9804331	NB4	blood:	n/a	chr12:9803552-9803562
8	RCOR1	chr12:9803270-9804348	GM12878	blood:	n/a	n/a
9	RELA	chr12:9803312-9804472	GM18526	blood:	n/a	n/a
10	MAX	chr12:9803341-9804341	GM12878	blood:	n/a	chr12:9803552-9803562
11	POLR2A	chr12:9799501-9804451	GM12891	blood:	n/a	n/a
12	YY1	chr12:9804013-9804270	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:9799408-9804409	GM19099	blood:	n/a	n/a
14	SPI1	chr12:9804062-9804263	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:9799328-9804610	GM12878	blood:	n/a	n/a
16	ATF2	chr12:9800087-9804473	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:9800142-9804355	GM18951	blood:	n/a	n/a
18	CBX3	chr12:9803724-9804484	K562	blood:	n/a	n/a
19	POLR2A	chr12:9799314-9804469	GM12892	blood:	n/a	n/a
20	SPI1	chr12:9803976-9804268	K562	blood:	n/a	n/a
21	MYC	chr12:9802846-9804368	K562	blood:	n/a	chr12:9803552-9803562
22	TAL1	chr12:9804193-9804374	K562	blood:	n/a	n/a
23	JUND	chr12:9803374-9804276	K562	blood:	n/a	n/a
24	EP300	chr12:9803289-9804338	GM12878	blood:	n/a	chr12:9803464-9803478 chr12:9803460-9803469
25	NFIC	chr12:9799779-9804349	GM12878	blood:	n/a	n/a
26	TBP	chr12:9803278-9804346	GM12878	blood:	n/a	n/a
27	RELA	chr12:9803258-9804469	GM10847	blood:	n/a	n/a
28	POLR2A	chr12:9799501-9804422	GM18526	blood:	n/a	n/a
29	MXI1	chr12:9803283-9804288	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:9799475-9804347	GM12892	blood:	n/a	n/a
31	POLR2A	chr12:9799681-9804387	Raji	blood:	n/a	n/a
32	SPI1	chr12:9804002-9804277	K562	blood:	n/a	n/a
33	MAZ	chr12:9803291-9804284	GM12878	blood:	n/a	n/a
34	RELA	chr12:9799625-9804451	GM19193	blood:	n/a	n/a
35	RELA	chr12:9799837-9804323	GM18505	blood:	n/a	n/a
36	TAF1	chr12:9804060-9804293	K562	blood:	n/a	n/a
37	GATA2	chr12:9804121-9804421	K562	blood:	n/a	n/a
38	ZNF143	chr12:9803924-9804395	K562	blood:	n/a	n/a
39	POLR2A	chr12:9804002-9804382	K562	blood:	n/a	n/a
40	RUNX3	chr12:9803209-9804465	GM12878	blood:	n/a	chr12:9803476-9803491
41	MTA3	chr12:9803869-9804581	GM12878	blood:	n/a	n/a
42	WRNIP1	chr12:9804161-9804361	GM12878	blood:	n/a	n/a
43	RELA	chr12:9799841-9804488	GM18951	blood:	n/a	n/a
44	POLR2A	chr12:9799520-9804579	GM12878	blood:	n/a	n/a
45	NFIC	chr12:9803053-9804359	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:9799517-9804360	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:9803951-9804324	GM12878	blood:	n/a	n/a
48	RUNX3	chr12:9802733-9804441	GM12878	blood:	n/a	chr12:9803476-9803491
49	ELF1	chr12:9803906-9804393	GM12878	blood:	n/a	chr12:9804144-9804157
50	POLR2A	chr12:9799348-9804458	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:
2	chr12:9802928..9804462-chr12:9806298..9808980,2	K562	blood:
3	chr12:9800783..9805047-chr12:9809567..9813940,5	K562	blood:
4	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:

Variant related genes	Relation type
ENSG00000256442	TF binding region
ENSG00000256594	TF binding region
ENSG00000256594	Chromatin interaction
ENSG00000256442	Chromatin interaction
ENSG00000257027	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10743798	0.83[AMR][1000 genomes]
rs10743801	1.00[AMR][1000 genomes]
rs1863872	0.92[AMR][1000 genomes]
rs2114868	1.00[AMR][1000 genomes]
rs2536823	1.00[MEX][hapmap]
rs3176782	1.00[MEX][hapmap]
rs4763262	0.85[AMR][1000 genomes]
rs59112803	1.00[AMR][1000 genomes]
rs60675581	0.85[AMR][1000 genomes]
rs6488065	0.91[YRI][hapmap]
rs7484445	1.00[MEX][hapmap]
rs7953065	0.89[YRI][hapmap]
rs7962958	0.84[YRI][hapmap]
rs988711	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9801000-9804400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr12:9801200-9804400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:9801400-9804400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:9801600-9811200	Weak transcription	Gastric	stomach
5	chr12:9801600-9815600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:9801800-9804400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:9802000-9805200	Flanking Active TSS	Dnd41	blood
8	chr12:9802200-9804400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr12:9802200-9806600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:9802200-9815200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:9802400-9804400	Enhancers	HUVEC	blood vessel
12	chr12:9802400-9806200	Weak transcription	A549	lung
13	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
14	chr12:9802600-9807200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:9802600-9812800	Weak transcription	Ovary	ovary
16	chr12:9802600-9814400	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:9802800-9804400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr12:9803000-9804600	Flanking Active TSS	GM12878-XiMat	blood
19	chr12:9803000-9805000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:9803000-9806000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:9803000-9806600	Weak transcription	Placenta	Placenta
22	chr12:9803000-9806600	Weak transcription	Psoas Muscle	Psoas
23	chr12:9803000-9811200	Weak transcription	Fetal Intestine Small	intestine
24	chr12:9803000-9812200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:9803000-9816400	Weak transcription	Brain Germinal Matrix	brain
26	chr12:9803000-9816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
28	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
29	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
30	chr12:9803200-9804400	Enhancers	Fetal Brain Male	brain
31	chr12:9803200-9804400	Enhancers	NHDF-Ad	bronchial
32	chr12:9803200-9812400	Weak transcription	Liver	Liver
33	chr12:9803200-9813400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:9803400-9804400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:9803400-9804400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:9803400-9804400	Flanking Active TSS	Fetal Thymus	thymus
37	chr12:9803400-9804400	Enhancers	Left Ventricle	heart
38	chr12:9803400-9804600	Enhancers	HMEC	breast
39	chr12:9803400-9804600	Enhancers	HSMM	muscle
40	chr12:9803400-9806200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr12:9803600-9804400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:9803600-9804400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr12:9803600-9804400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:9803600-9804400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr12:9803600-9804400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr12:9803600-9804400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr12:9803600-9804400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr12:9803600-9804400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr12:9803600-9804400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr12:9803600-9804400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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