Variant report

Variant	rs6487574
Chromosome Location	chr12:9218000-9218001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:88)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:88 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr12:9216672-9218117	ECC-1	luminal epithelium:	n/a	chr12:9217642-9217653
2	MAZ	chr12:9216723-9218224	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:9216895-9230988	HepG2	liver:	n/a	n/a
4	BRCA1	chr12:9217820-9218140	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:9217182-9218135	H1-hESC	embryonic stem cell:	n/a	n/a
6	TBP	chr12:9216751-9218037	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:9216620-9218145	HCT-116	colon:	n/a	n/a
8	MAX	chr12:9217296-9218038	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr12:9217880-9218030	SAEC	small airway:	n/a	n/a
10	POLR2A	chr12:9217762-9218201	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:9216745-9218074	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:9216806-9219983	HepG2	liver:	n/a	n/a
13	CHD2	chr12:9217996-9219810	HepG2	liver:	n/a	n/a
14	MYBL2	chr12:9217292-9218061	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr12:9216688-9218046	MCF-7	breast:	n/a	n/a
16	TCF7L2	chr12:9216780-9218026	HCT-116	colon:	n/a	n/a
17	POLR2A	chr12:9216389-9221070	HepG2	liver:	n/a	n/a
18	POLR2A	chr12:9216782-9218494	HepG2	liver:	n/a	n/a
19	MBD4	chr12:9217946-9218417	HepG2	liver:	n/a	n/a
20	HDAC2	chr12:9217440-9218080	MCF-7	breast:	n/a	n/a
21	JUN	chr12:9217925-9218110	H1-hESC	embryonic stem cell:	n/a	n/a
22	NR2C2	chr12:9217015-9218395	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr12:9217762-9218069	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:9217415-9220251	HepG2	liver:	n/a	n/a
25	MAX	chr12:9216705-9218112	MCF-7	breast:	n/a	n/a
26	TCF12	chr12:9216607-9218377	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr12:9216589-9220417	HepG2	liver:	n/a	n/a
28	RAD21	chr12:9217463-9218066	H1-hESC	embryonic stem cell:	n/a	n/a
29	BACH1	chr12:9216722-9218327	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr12:9216772-9218342	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr12:9216730-9218156	HCT-116	colon:	n/a	n/a
32	TAF1	chr12:9216803-9218264	HepG2	liver:	n/a	n/a
33	POLR2A	chr12:9216189-9218094	MCF10A-Er-Src	breast:	n/a	n/a
34	MBD4	chr12:9217357-9218058	HepG2	liver:	n/a	n/a
35	MYBL2	chr12:9217745-9218093	HepG2	liver:	n/a	n/a
36	MAX	chr12:9217200-9218412	HepG2	liver:	n/a	n/a
37	EP300	chr12:9216701-9218037	ECC-1	luminal epithelium:	n/a	chr12:9217646-9217662
38	TEAD4	chr12:9216707-9218185	ECC-1	luminal epithelium:	n/a	n/a
39	HEY1	chr12:9216729-9218119	HepG2	liver:	n/a	chr12:9217615-9217630
40	CTBP2	chr12:9216782-9218277	H1-hESC	embryonic stem cell:	n/a	n/a
41	TFAP2C	chr12:9216773-9218143	Hela-S3	cervix:	n/a	chr12:9217567-9217582
42	RCOR1	chr12:9216671-9218459	Hela-S3	cervix:	n/a	n/a
43	MAX	chr12:9216737-9218529	HepG2	liver:	n/a	n/a
44	GABPA	chr12:9217125-9218097	MCF-7	breast:	n/a	n/a
45	POLR2A	chr12:9216491-9218217	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr12:9216657-9218399	MCF-7	breast:	n/a	n/a
47	HCFC1	chr12:9216165-9218175	Hela-S3	cervix:	n/a	n/a
48	JUND	chr12:9217747-9218356	HepG2	liver:	n/a	n/a
49	RFX5	chr12:9217924-9218475	HepG2	liver:	n/a	n/a
50	MXI1	chr12:9216742-9218293	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9064962..9066827-chr12:9216213..9218614,2	MCF-7	breast:
2	chr12:9100379..9103293-chr12:9215519..9218225,4	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00612	TF binding region
ENSG00000111752	Chromatin interaction
ENSG00000003056	Chromatin interaction
ENSG00000139187	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10771307	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771309	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771310	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842789	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842795	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842820	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842845	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842898	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11048789	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805651	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805652	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805653	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805654	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805655	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805656	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805657	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805658	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805659	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805660	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805662	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs1805663	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs1805664	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805666	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805667	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805678	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805681	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2193005	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs226379	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs226383	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs226384	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs226393	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs226395	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2300147	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300148	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2377682	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487581	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487585	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487587	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135781	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7299282	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7299600	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7309361	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310089	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310167	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310884	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310921	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955940	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965184	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968640	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7976461	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881376	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS 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 miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:145 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9216200-9218400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr12:9216400-9218000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:9216400-9218000	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr12:9216600-9218000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr12:9216600-9218000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr12:9216600-9218000	Active TSS	Fetal Stomach	stomach
7	chr12:9216600-9218000	Active TSS	Ovary	ovary
8	chr12:9216600-9218000	Active TSS	Right Ventricle	heart
9	chr12:9216600-9218200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr12:9216600-9218200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:9216600-9218200	Active TSS	Psoas Muscle	Psoas
12	chr12:9216600-9218200	Active TSS	Right Atrium	heart
13	chr12:9216600-9218400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr12:9216600-9218400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:9216600-9218600	Active TSS	Brain Angular Gyrus	brain
16	chr12:9216600-9218600	Active TSS	NHLF	lung
17	chr12:9216800-9218000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:9216800-9218000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:9216800-9218000	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr12:9216800-9218000	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr12:9216800-9218000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:9216800-9218000	Active TSS	Brain Anterior Caudate	brain
23	chr12:9216800-9218000	Active TSS	Colon Smooth Muscle	Colon
24	chr12:9216800-9218000	Active TSS	Fetal Heart	heart
25	chr12:9216800-9218000	Active TSS	Lung	lung
26	chr12:9216800-9218000	Active TSS	Pancreas	Pancrea
27	chr12:9216800-9218000	Active TSS	Rectal Smooth Muscle	rectum
28	chr12:9216800-9218000	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr12:9216800-9218000	Active TSS	Spleen	Spleen
30	chr12:9216800-9218000	Active TSS	HSMMtube	muscle
31	chr12:9216800-9218000	Active TSS	NH-A	brain
32	chr12:9216800-9218000	Active TSS	NHDF-Ad	bronchial
33	chr12:9216800-9218200	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr12:9216800-9218200	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr12:9216800-9218200	Active TSS	Muscle Satellite Cultured Cells	--
36	chr12:9216800-9218200	Active TSS	Aorta	Aorta
37	chr12:9216800-9218200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:9216800-9218200	Active TSS	Duodenum Mucosa	Duodenum
39	chr12:9216800-9218200	Active TSS	Fetal Kidney	kidney
40	chr12:9216800-9218200	Active TSS	HepG2	liver
41	chr12:9216800-9218400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr12:9216800-9218400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:9216800-9218400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:9216800-9218400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:9216800-9218400	Active TSS	Brain Cingulate Gyrus	brain
46	chr12:9216800-9218400	Active TSS	Brain Hippocampus Middle	brain
47	chr12:9216800-9218400	Active TSS	Brain Substantia Nigra	brain
48	chr12:9216800-9218400	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr12:9216800-9218400	Active TSS	A549	lung
50	chr12:9216800-9218400	Active TSS	Osteobl	bone

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