Variant report

Variant	rs11061928
Chromosome Location	chr12:1807323-1807324
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:1807220-1807370	SK-N-SH_RA	brain:	n/a	n/a
2	TCF7L2	chr12:1807179-1807529	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr12:1807316-1807345	MCF-7	breast:	n/a	n/a
4	ZNF274	chr12:1807265-1807335	NT2-D1	testis:	n/a	n/a
5	POLR2A	chr12:1807269-1807667	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:1807305-1807355	SK-N-MC	brain:	n/a
2	chr12:1807305-1807355	ovcar-3	ovarian:	n/a
3	chr12:1807305-1807355	HCF	heart:	n/a
4	chr12:1807305-1807355	GM12892	blood:	n/a
5	chr12:1807305-1807355	Jurkat	blood:	n/a
6	chr12:1807305-1807355	GM12878	blood:	n/a
7	chr12:1807305-1807355	A549	lung:	n/a
8	chr12:1807305-1807355	NHDF-neo	bronchial:	n/a
9	chr12:1807305-1807355	HNPCEpiC	eye:	n/a
10	chr12:1807305-1807355	AG10803	skin:	n/a
11	chr12:1807305-1807355	HPAEpiC	pulmonary alveolar:	n/a
12	chr12:1807305-1807355	HIPEpiC	eye:	n/a
13	chr12:1807305-1807355	SK-N-SH	brain:	n/a
14	chr12:1807305-1807355	ProgFib	skin:	n/a
15	chr12:1807305-1807355	PANC-1	pancreas:	n/a
16	chr12:1807305-1807355	HepG2	liver:	n/a
17	chr12:1807305-1807355	MCF10A-Er-Src	breast:	n/a
18	chr12:1807305-1807355	AG04449	skin:	fetal
19	chr12:1807305-1807355	SK-N-SH_RA	brain:	n/a
20	chr12:1807305-1807355	SKMC	muscle:	n/a
21	chr12:1807305-1807355	NT2-D1	testis:	n/a
22	chr12:1807305-1807355	CMK	blood:	n/a
23	chr12:1807305-1807355	HAEpiC	amniotic membrane:	n/a
24	chr12:1807305-1807355	BE2_C	brain:	n/a
25	chr12:1807305-1807355	HRCEpiC	kidney:	n/a
26	chr12:1807305-1807355	HRPEpiC	eye:	n/a
27	chr12:1807305-1807355	HCM	heart:	n/a
28	chr12:1807305-1807355	HL-60	blood:	n/a
29	chr12:1807305-1807355	K562	blood:	n/a
30	chr12:1807305-1807355	AG09309	skin:	n/a
31	chr12:1807305-1807355	U87	brain:	n/a
32	chr12:1807305-1807355	HEK293	kidney:	embryo
33	chr12:1807305-1807355	HRE	kidney:	n/a
34	chr12:1807305-1807355	RPTEC	kidney:	n/a
35	chr12:1807305-1807355	IMR90	lung:	fetal
36	chr12:1807305-1807355	HCPEpiC	choroid plexus:	n/a
37	chr12:1807305-1807355	Caco-2	colon:	n/a
38	chr12:1807305-1807355	T-47D	breast:	n/a
39	chr12:1807305-1807355	HEEpiC	esophagus:	n/a
40	chr12:1807305-1807355	GM06990	blood:	n/a
41	chr12:1807305-1807355	Hepatocyte	liver:	n/a
42	chr12:1807305-1807355	AG09319	gingival:	n/a
43	chr12:1807305-1807355	HMEC	breast:	n/a
44	chr12:1807305-1807355	PrEC	prostate:	n/a
45	chr12:1807305-1807355	PFSK-1	brain:	n/a
46	chr12:1807305-1807355	AG04450	lung:	fetal
47	chr12:1807305-1807355	MCF-7	breast:	n/a
48	chr12:1807305-1807355	NB4	blood:	n/a
49	chr12:1807305-1807355	Hela-S3	cervix:	n/a
50	chr12:1807305-1807355	H1-hESC	embryonic stem cell:	embryo

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1805184..1807328-chr12:1869608..1872383,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271500	TF binding region
ENSG00000271500	CpG island
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10491959	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10848555	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11061931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][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]
rs11061932	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];0.97[MKK][hapmap];1.00[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]
rs11061934	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061938	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061939	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061941	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061943	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061944	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061947	0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11061949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11061955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061958	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061959	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11061961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061963	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061975	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11061979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11061980	1.00[YRI][hapmap]
rs11608456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610397	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11610411	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11610838	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11612238	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612414	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs11612726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11614622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12229061	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12229999	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230349	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230994	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2041139	1.00[GIH][hapmap];0.84[MKK][hapmap]
rs2286382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2369975	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58500393	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61153802	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6489322	0.95[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	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1045312	chr12:1805856-1843202	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1801000-1815800	Weak transcription	Esophagus	oesophagus
2	chr12:1801000-1815800	Weak transcription	Gastric	stomach
3	chr12:1801600-1807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:1801600-1814200	Weak transcription	HSMM	muscle
5	chr12:1801600-1815200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:1801600-1823400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:1801600-1827800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:1801800-1807800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:1801800-1808200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:1801800-1811400	Weak transcription	NH-A	brain
11	chr12:1801800-1813400	Weak transcription	A549	lung
12	chr12:1801800-1823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:1801800-1828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:1801800-1830800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:1802200-1807800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:1802200-1815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:1802200-1815000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:1802200-1815000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:1802200-1815400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:1802200-1815800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:1802200-1822800	Weak transcription	Thymus	Thymus
22	chr12:1802400-1808800	Weak transcription	HUVEC	blood vessel
23	chr12:1802400-1811800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:1802400-1815000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:1802400-1822800	Weak transcription	Fetal Thymus	thymus
26	chr12:1802400-1823000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:1802400-1824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:1802400-1841200	Weak transcription	HMEC	breast
29	chr12:1802600-1808000	Enhancers	Adipose Nuclei	Adipose
30	chr12:1803000-1813400	Weak transcription	Primary B cells from cord blood	blood
31	chr12:1803200-1815800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr12:1803600-1808400	Enhancers	Brain Hippocampus Middle	brain
33	chr12:1803600-1808400	Enhancers	HepG2	liver
34	chr12:1803800-1812400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:1804400-1808800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:1804400-1809400	Enhancers	Stomach Mucosa	stomach
37	chr12:1804400-1816000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:1804600-1810200	Weak transcription	Fetal Intestine Small	intestine
39	chr12:1804800-1807400	Enhancers	Brain Anterior Caudate	brain
40	chr12:1805000-1807400	Enhancers	Brain Substantia Nigra	brain
41	chr12:1805000-1807600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr12:1805000-1808200	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr12:1805000-1809200	Enhancers	Liver	Liver
44	chr12:1805200-1807600	Enhancers	Psoas Muscle	Psoas
45	chr12:1805200-1807600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr12:1805200-1807800	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr12:1805200-1808000	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr12:1805200-1808200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr12:1805200-1808400	Enhancers	Hela-S3	cervix
50	chr12:1805400-1808400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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