Variant report

Variant	rs7485650
Chromosome Location	chr12:57609445-57609446
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	CTCF	chr12:57609401-57609527	NHEK	skin:	n/a	n/a
2	MAZ	chr12:57609115-57611710	IMR90	lung:	n/a	chr12:57610318-57610327
3	POLR2A	chr12:57609203-57610337	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr12:57606903-57610506	U87	brain:	n/a	n/a
5	RFX5	chr12:57609310-57610085	GM12878	blood:	n/a	chr12:57609655-57609664 chr12:57609652-57609667 chr12:57609653-57609667
6	POLR2A	chr12:57607153-57610401	U87	brain:	n/a	n/a
7	TCF3	chr12:57609271-57609814	GM12878	blood:	n/a	chr12:57609432-57609441 chr12:57609430-57609444
8	CTCF	chr12:57609380-57609530	GM12873	blood:	n/a	n/a
9	CTCF	chr12:57609444-57609506	GM19238	blood:	n/a	n/a
10	ZNF263	chr12:57609221-57610004	HEK293-T-REx	kidney:	n/a	chr12:57609709-57609730
11	POLR2A	chr12:57609212-57610573	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr12:57607241-57609488	HepG2	liver:	n/a	n/a
13	CTCF	chr12:57609407-57609572	GM12891	blood:	n/a	n/a
14	POLR2A	chr12:57606909-57610500	U87	brain:	n/a	n/a
15	RUNX3	chr12:57609410-57609954	GM12878	blood:	n/a	n/a
16	RFX5	chr12:57607830-57610239	SK-N-SH	brain:	n/a	chr12:57609655-57609664 chr12:57609652-57609667 chr12:57609653-57609667
17	RFX5	chr12:57606888-57610516	IMR90	lung:	n/a	chr12:57609655-57609664 chr12:57609652-57609667 chr12:57609653-57609667
18	POLR2A	chr12:57609376-57609455	ProgFib	skin:	n/a	n/a
19	CTBP2	chr12:57609400-57610511	H1-hESC	embryonic stem cell:	n/a	n/a
20	BRCA1	chr12:57609361-57609487	HepG2	liver:	n/a	n/a
21	RFX5	chr12:57609194-57610153	HepG2	liver:	n/a	chr12:57609655-57609664 chr12:57609652-57609667 chr12:57609653-57609667
22	ZEB1	chr12:57609249-57609582	GM12878	blood:	n/a	chr12:57609433-57609442 chr12:57609319-57609331
23	MTA3	chr12:57609299-57610013	GM12878	blood:	n/a	n/a
24	CTCF	chr12:57609426-57609543	GM19239	blood:	n/a	n/a
25	POLR2A	chr12:57609208-57609732	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr12:57609386-57609558	GM12892	blood:	n/a	n/a
27	CTCF	chr12:57609420-57609570	HEK293	kidney:	n/a	n/a
28	CREB1	chr12:57609420-57609948	GM12878	blood:	n/a	n/a
29	CTCF	chr12:57609300-57609450	HA-sp	spinal cord:	n/a	n/a
30	RUNX3	chr12:57609419-57609865	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:57607153-57610353	U87	brain:	n/a	n/a
32	CREB1	chr12:57609384-57610066	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57606014..57610025-chr12:57631623..57633806,36	MCF-7	breast:
2	chr12:57607877..57611743-chr12:57643490..57646687,3	K562	blood:
3	chr12:57595870..57598070-chr12:57607882..57609452,2	K562	blood:
4	chr12:57608303..57611284-chr12:57611816..57613934,2	MCF-7	breast:
5	chr12:57606546..57610160-chr12:57612220..57614034,3	K562	blood:

Variant related genes	Relation type
NXPH4	TF binding region
ENSG00000182379	Chromatin interaction
ENSG00000185482	Chromatin interaction
ENSG00000123384	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs34399241	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7134826	1.00[CHB][hapmap]
rs7977876	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv525873	chr12:57535266-57616013	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv869636	chr12:57590172-57613714	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv899116	chr12:57597169-57623363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57603200-57610200	Weak transcription	Right Atrium	heart
2	chr12:57606400-57610200	Weak transcription	Aorta	Aorta
3	chr12:57606800-57609600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr12:57606800-57609600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:57606800-57609600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:57606800-57609800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr12:57606800-57610200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
8	chr12:57606800-57610200	Enhancers	Pancreas	Pancrea
9	chr12:57607000-57609800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:57607200-57609600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:57607200-57610000	Enhancers	Right Ventricle	heart
12	chr12:57607200-57610800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr12:57607400-57609600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr12:57607400-57609600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:57607400-57609600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
16	chr12:57607400-57609600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
17	chr12:57607400-57609800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
18	chr12:57607400-57609800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
19	chr12:57607400-57610200	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr12:57607600-57609800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
21	chr12:57607600-57610200	Weak transcription	Ovary	ovary
22	chr12:57607800-57609600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
23	chr12:57607800-57609800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:57607800-57610200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr12:57608000-57609600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:57608000-57609800	Enhancers	HSMMtube	muscle
27	chr12:57608000-57610200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:57608000-57610600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr12:57608400-57609800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:57608400-57609800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:57608400-57610200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:57608400-57610200	Bivalent Enhancer	Esophagus	oesophagus
33	chr12:57608400-57610200	Bivalent Enhancer	Placenta	Placenta
34	chr12:57608600-57609600	Bivalent Enhancer	Brain Germinal Matrix	brain
35	chr12:57608600-57609600	Bivalent Enhancer	HepG2	liver
36	chr12:57608600-57609800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
37	chr12:57608600-57609800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
38	chr12:57608600-57609800	Bivalent Enhancer	A549	lung
39	chr12:57608600-57610200	Bivalent Enhancer	Fetal Brain Male	brain
40	chr12:57608600-57610200	Enhancers	Spleen	Spleen
41	chr12:57608800-57609800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:57608800-57609800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:57608800-57610200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:57609000-57609800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
45	chr12:57609000-57610200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:57609200-57609600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:57609200-57609600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:57609200-57609600	Bivalent Enhancer	Adipose Nuclei	Adipose
49	chr12:57609200-57609600	Bivalent Enhancer	Colon Smooth Muscle	Colon
50	chr12:57609200-57609600	Bivalent Enhancer	NHEK	skin

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