Variant report

Variant	rs28365179
Chromosome Location	chr12:40501033-40501034
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	CTCF	chr12:40500940-40501090	WERI-Rb-1	eye:	n/a	n/a
2	GATA3	chr12:40500917-40501724	MCF-7	breast:	n/a	n/a
3	TCF12	chr12:40500905-40501778	A549	lung:	n/a	n/a
4	CTCF	chr12:40500864-40501083	MCF-7	breast:	n/a	n/a
5	CTCF	chr12:40501003-40501046	Spleen_OC	spleen:	n/a	n/a
6	MYC	chr12:40500779-40501080	MCF-7	breast:	n/a	n/a
7	STAT3	chr12:40500966-40501236	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr12:40500940-40501090	HRE	kidney:	n/a	n/a
9	SIN3AK20	chr12:40500931-40501822	MCF-7	breast:	n/a	n/a
10	GATA3	chr12:40500971-40501707	SK-N-SH	brain:	n/a	n/a
11	CEBPB	chr12:40501016-40501656	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr12:40500940-40501090	HPAF	blood vessel:	n/a	n/a
13	CTCF	chr12:40500871-40501050	MCF-7	breast:	n/a	n/a
14	KAP1	chr12:40500195-40501769	HEK293	kidney:	n/a	n/a
15	CTCF	chr12:40500980-40501230	AoAF	blood vessel:	n/a	n/a
16	TCF7L2	chr12:40500799-40501717	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr12:40500940-40501090	WI-38	lung:	n/a	n/a
18	CTCF	chr12:40500920-40501070	Caco-2	colon:	n/a	n/a
19	MYC	chr12:40500961-40501107	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:40500694-40501181	MCF-7	breast:	n/a	n/a
21	GATA2	chr12:40500852-40501552	SH-SY5Y	brain:	n/a	n/a
22	POLR2A	chr12:40500683-40501171	MCF-7	breast:	n/a	n/a
23	CTCF	chr12:40500940-40501090	MCF-7	breast:	n/a	n/a
24	CTCF	chr12:40500980-40501130	HPF	lung:	n/a	n/a
25	MYC	chr12:40500962-40501096	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:40500869-40501036	Gliobla	brain:	n/a	n/a
27	RAD21	chr12:40500883-40501897	SK-N-SH	brain:	n/a	chr12:40501509-40501528 chr12:40501513-40501523 chr12:40501511-40501523
28	MXI1	chr12:40500952-40501858	SK-N-SH	brain:	n/a	n/a
29	CTCF	chr12:40500857-40501079	MCF-7	breast:	n/a	n/a
30	RAD21	chr12:40500967-40501734	IMR90	lung:	n/a	chr12:40501509-40501528 chr12:40501513-40501523 chr12:40501511-40501523
31	MYC	chr12:40500791-40501128	MCF-7	breast:	n/a	n/a
32	CTCF	chr12:40500900-40501050	GM12873	blood:	n/a	n/a
33	KAP1	chr12:40500753-40501728	U2OS	brain:	n/a	n/a
34	RCOR1	chr12:40500887-40501814	IMR90	lung:	n/a	n/a
35	POLR2A	chr12:40500848-40501058	MCF-7	breast:	n/a	n/a
36	CTCF	chr12:40500900-40501050	HAc	cerebellar:	n/a	n/a
37	MYC	chr12:40500873-40501137	HUVEC	blood vessel:	n/a	n/a
38	CTCF	chr12:40500940-40501090	GM12869	blood:	n/a	n/a
39	GATA3	chr12:40501021-40501730	T-47D	breast:	n/a	n/a
40	CTCF	chr12:40500940-40501090	GM06990	blood:	n/a	n/a
41	CTCF	chr12:40500893-40501067	ProgFib	skin:	n/a	n/a
42	HA-E2F1	chr12:40500814-40501768	MCF-7	breast:	n/a	chr12:40501478-40501493 chr12:40501468-40501482 chr12:40501471-40501485 chr12:40501476-40501483
43	CTCF	chr12:40500960-40501110	HRPEpiC	eye:	n/a	n/a
44	CTCF	chr12:40500862-40501070	MCF-7	breast:	n/a	n/a
45	CTCF	chr12:40500980-40501130	GM12865	blood:	n/a	n/a
46	CTCF	chr12:40500960-40501034	MCF-7	breast:	n/a	n/a
47	CTCF	chr12:40500940-40501090	GM12878	blood:	n/a	n/a
48	GATA3	chr12:40500980-40501819	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:40404217..40405558-chr12:40500388..40503110,15	MCF-7	breast:
2	chr12:40413403..40416172-chr12:40500145..40501731,2	K562	blood:
3	chr12:40158518..40159407-chr12:40501012..40501936,2	K562	blood:

Variant related genes	Relation type
SLC2A13	TF binding region

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10506148	0.81[CHB][hapmap]
rs10784340	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10877913	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10877955	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10877971	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10878123	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174831	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11174928	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11175102	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11175103	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11175256	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11175260	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11175332	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11175371	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11175401	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11175422	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs11175540	0.90[EUR][1000 genomes]
rs11175558	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11564115	0.94[JPT][hapmap]
rs12372213	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12581285	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1472117	0.89[JPT][hapmap]
rs1491924	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes]
rs1491942	0.84[JPT][hapmap]
rs17442157	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17443199	0.82[CHB][hapmap]
rs17458156	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17458613	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17461429	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17518546	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2131088	0.89[JPT][hapmap]
rs2201144	0.94[JPT][hapmap]
rs2638244	0.85[JPT][hapmap]
rs2638270	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2638271	0.85[JPT][hapmap]
rs2708437	0.94[JPT][hapmap]
rs2708438	0.94[JPT][hapmap]
rs2708478	0.80[EUR][1000 genomes]
rs2723269	0.89[JPT][hapmap]
rs28365172	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28365683	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28370683	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72644819	0.92[EUR][1000 genomes]
rs949640	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3436452	chr12:40498510-40501058	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
7	esv1846566	chr12:40498683-40527395	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv1838306	chr12:40499495-40527395	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40496800-40501600	Active TSS	Brain Cingulate Gyrus	brain
2	chr12:40496800-40501600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:40496800-40501600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:40497000-40501600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr12:40497000-40501600	Active TSS	Fetal Kidney	kidney
6	chr12:40497200-40502200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:40497400-40501600	Active TSS	Right Atrium	heart
8	chr12:40497800-40501400	Active TSS	Brain Substantia Nigra	brain
9	chr12:40497800-40501400	Active TSS	Sigmoid Colon	Sigmoid Colon
10	chr12:40498000-40501600	Active TSS	Ovary	ovary
11	chr12:40498200-40501800	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr12:40498200-40501800	Active TSS	NHLF	lung
13	chr12:40498400-40501600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:40498600-40501600	Active TSS	Aorta	Aorta
15	chr12:40498800-40501600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:40498800-40501600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:40499000-40501400	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr12:40499000-40501400	Active TSS	Colonic Mucosa	Colon
19	chr12:40499000-40501400	Active TSS	Esophagus	oesophagus
20	chr12:40499000-40501400	Active TSS	Left Ventricle	heart
21	chr12:40499000-40501600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:40499000-40501600	Active TSS	Brain Anterior Caudate	brain
23	chr12:40499000-40501600	Active TSS	Duodenum Mucosa	Duodenum
24	chr12:40499200-40501400	Active TSS	Fetal Muscle Leg	muscle
25	chr12:40499200-40501600	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr12:40499200-40501600	Active TSS	NH-A	brain
27	chr12:40499800-40501600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:40499800-40501600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:40499800-40501600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:40500000-40501200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr12:40500000-40501200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr12:40500000-40501200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:40500000-40501400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr12:40500000-40501400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr12:40500000-40501400	Flanking Active TSS	Hela-S3	cervix
36	chr12:40500000-40501400	Flanking Active TSS	HMEC	breast
37	chr12:40500000-40501600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr12:40500200-40501400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:40500200-40501400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr12:40500200-40501400	Flanking Active TSS	NHEK	skin
41	chr12:40500200-40502200	Enhancers	Placenta	Placenta
42	chr12:40500400-40501200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:40500400-40501200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
44	chr12:40500400-40501200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
45	chr12:40500400-40501200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
46	chr12:40500400-40501200	Active TSS	Primary T cells from cord blood	blood
47	chr12:40500400-40501200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr12:40500400-40501200	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr12:40500400-40501200	Enhancers	Gastric	stomach
50	chr12:40500400-40501200	Flanking Active TSS	Stomach Smooth Muscle	stomach

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