Variant report

Variant	rs6580638
Chromosome Location	chr12:48207950-48207951
allele	A/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	MAX	chr12:48206221-48208131	NB4	blood:	n/a	n/a
2	RUNX3	chr12:48206618-48208191	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:48206469-48208700	K562	blood:	n/a	n/a
4	MYC	chr12:48206188-48207983	NB4	blood:	n/a	n/a
5	POLR2A	chr12:48206263-48208150	GM12878	blood:	n/a	n/a
6	ZNF263	chr12:48207107-48209086	HEK293-T-REx	kidney:	n/a	chr12:48208231-48208240 chr12:48207277-48207286 chr12:48208242-48208263 chr12:48208434-48208443
7	POLR2A	chr12:48206402-48208023	GM18505	blood:	n/a	n/a
8	BCLAF1	chr12:48207537-48208078	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:48207820-48208145	MCF10A-Er-Src	breast:	n/a	n/a
10	ELF1	chr12:48206530-48208165	GM12878	blood:	n/a	chr12:48206985-48206997
11	RELA	chr12:48206375-48208011	GM19193	blood:	n/a	n/a
12	POLR2A	chr12:48206953-48208134	GM12892	blood:	n/a	n/a
13	RELA	chr12:48206402-48208005	GM12891	blood:	n/a	n/a
14	RCOR1	chr12:48203929-48208034	IMR90	lung:	n/a	n/a
15	MAZ	chr12:48207629-48208022	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:48206619-48208020	GM15510	blood:	n/a	n/a
17	POLR2A	chr12:48207027-48208399	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:48206580-48208043	GM12892	blood:	n/a	n/a
19	NFATC1	chr12:48207509-48208080	GM12878	blood:	n/a	n/a
20	NR2F2	chr12:48207445-48207975	K562	blood:	n/a	n/a
21	POLR2A	chr12:48207434-48208111	ECC-1	luminal epithelium:	n/a	n/a
22	TBL1XR1	chr12:48207746-48207956	K562	blood:	n/a	n/a
23	POLR2A	chr12:48206337-48208251	Raji	blood:	n/a	n/a
24	POLR2A	chr12:48206212-48208617	H1-hESC	embryonic stem cell:	n/a	n/a
25	RELA	chr12:48206376-48208001	GM18951	blood:	n/a	n/a
26	POLR2A	chr12:48206442-48208619	GM12878	blood:	n/a	n/a
27	ELF1	chr12:48206541-48208064	GM12878	blood:	n/a	chr12:48206985-48206997
28	POLR2A	chr12:48206213-48209030	GM12892	blood:	n/a	n/a
29	MTA3	chr12:48205364-48208488	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:48206482-48208206	GM12892	blood:	n/a	n/a
31	MAZ	chr12:48205318-48208032	IMR90	lung:	n/a	n/a
32	PML	chr12:48206409-48208025	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:48206533-48208000	GM12878	blood:	n/a	n/a
34	STAT5A	chr12:48206255-48208560	GM12878	blood:	n/a	chr12:48206974-48206986 chr12:48207721-48207733 chr12:48207277-48207285
35	TCF3	chr12:48207400-48208021	GM12878	blood:	n/a	n/a
36	ATF2	chr12:48207502-48208063	GM12878	blood:	n/a	n/a
37	EBF1	chr12:48207611-48208003	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:48206443-48208310	NB4	blood:	n/a	n/a
39	NFIC	chr12:48206464-48208067	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:48206953-48208050	GM12891	blood:	n/a	n/a
41	EBF1	chr12:48207635-48207958	GM12878	blood:	n/a	n/a
42	RCOR1	chr12:48206394-48207996	GM12878	blood:	n/a	n/a
43	TCF12	chr12:48207670-48207987	GM12878	blood:	n/a	chr12:48207735-48207745
44	POLR2A	chr12:48206276-48208154	GM12878	blood:	n/a	n/a
45	POLR2A	chr12:48206107-48208260	GM12892	blood:	n/a	n/a
46	ZNF143	chr12:48207796-48207964	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:48207899-48207986	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr12:48206542-48208126	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48194186..48197622-chr12:48205034..48208393,5	K562	blood:
2	chr12:48099357..48101447-chr12:48205677..48208435,2	K562	blood:
3	chr12:48165044..48167093-chr12:48206926..48209042,2	K562	blood:
4	chr12:48099357..48102097-chr12:48206829..48208435,2	K562	blood:

Variant related genes	Relation type
HDAC7	TF binding region
ENSG00000257433	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11837686	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814620	1.00[ASN][1000 genomes]
rs12820931	1.00[ASN][1000 genomes]
rs12828203	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828577	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122326	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34248545	1.00[ASN][1000 genomes]
rs34379708	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34785684	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35392237	1.00[ASN][1000 genomes]
rs71462981	1.00[ASN][1000 genomes]
rs7299689	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303453	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980930	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	esv3693398	chr12:48186738-48215749	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	esv999028	chr12:48199301-48209132	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 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	chr12:48202400-48208200	Weak transcription	Ovary	ovary
2	chr12:48203600-48208400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr12:48203800-48208200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48203800-48209000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:48203800-48209200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:48204000-48209400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
7	chr12:48204200-48208600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr12:48204200-48209600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:48204800-48208200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48205000-48208600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr12:48205200-48208600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr12:48205400-48211800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:48205600-48208800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr12:48205800-48208000	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr12:48205800-48208200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr12:48205800-48208400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:48205800-48209000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr12:48206200-48208200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr12:48206400-48208000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:48206400-48208000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:48206400-48208800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:48206400-48209200	Enhancers	Liver	Liver
23	chr12:48206800-48208600	Enhancers	Pancreas	Pancrea
24	chr12:48206800-48209400	Enhancers	Small Intestine	intestine
25	chr12:48206800-48209400	Transcr. at gene 5' and 3'	Thymus	Thymus
26	chr12:48207000-48208000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr12:48207000-48208000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr12:48207000-48208000	Flanking Active TSS	HUVEC	blood vessel
29	chr12:48207000-48208200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:48207000-48208200	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr12:48207000-48208200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:48207000-48208200	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr12:48207000-48208200	Flanking Active TSS	GM12878-XiMat	blood
34	chr12:48207000-48208400	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr12:48207000-48208400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr12:48207000-48208400	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr12:48207000-48208400	Flanking Active TSS	Colonic Mucosa	Colon
38	chr12:48207000-48209000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr12:48207000-48209200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:48207000-48209600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:48207200-48208000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr12:48207200-48208200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:48207200-48208200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:48207200-48208200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr12:48207200-48208200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:48207200-48208200	Flanking Active TSS	K562	blood
47	chr12:48207200-48208200	Transcr. at gene 5' and 3'	NHLF	lung
48	chr12:48207200-48208400	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr12:48207200-48208600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:48207200-48208600	Flanking Active TSS	Primary T cells from cord blood	blood

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