Variant report

Variant	rs7302081
Chromosome Location	chr12:9800926-9800927
allele	C/T
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	STAT1	chr12:9800284-9801263	GM12878	blood:	n/a	chr12:9800489-9800496 chr12:9800768-9800780
2	PAX5	chr12:9800772-9801173	GM12891	blood:	n/a	chr12:9800961-9800980
3	GABPA	chr12:9800275-9801002	A549	lung:	n/a	n/a
4	MXI1	chr12:9800287-9802771	GM12878	blood:	n/a	n/a
5	GABPA	chr12:9800034-9801209	A549	lung:	n/a	n/a
6	GABPA	chr12:9800316-9801165	HL-60	blood:	n/a	n/a
7	UBTF	chr12:9800050-9801395	K562	blood:	n/a	n/a
8	STAT3	chr12:9800692-9801447	GM12878	blood:	n/a	chr12:9800768-9800780
9	MYC	chr12:9800560-9801184	MCF10A-Er-Src	breast:	n/a	n/a
10	BRCA1	chr12:9800286-9801460	Hela-S3	cervix:	n/a	n/a
11	CHD1	chr12:9800337-9804156	GM12878	blood:	n/a	chr12:9800667-9800677 chr12:9800660-9800670
12	TBL1XR1	chr12:9799984-9802966	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:9799451-9804403	GM19193	blood:	n/a	n/a
14	MAX	chr12:9800424-9801178	A549	lung:	n/a	n/a
15	TBP	chr12:9800698-9801701	GM12878	blood:	n/a	n/a
16	TAF1	chr12:9800589-9801123	GM12892	blood:	n/a	n/a
17	EP300	chr12:9800236-9801592	ECC-1	luminal epithelium:	n/a	chr12:9800672-9800688 chr12:9800673-9800689
18	RUNX3	chr12:9799672-9801651	GM12878	blood:	n/a	chr12:9800805-9800822
19	POLR2A	chr12:9800283-9801270	Hela-S3	cervix:	n/a	n/a
20	MTA3	chr12:9799406-9804477	GM12878	blood:	n/a	n/a
21	JUND	chr12:9800476-9800993	H1-hESC	embryonic stem cell:	n/a	chr12:9800672-9800681
22	MAX	chr12:9800358-9801415	SK-N-SH	brain:	n/a	n/a
23	YY1	chr12:9800447-9801045	K562	blood:	n/a	chr12:9800569-9800580 chr12:9800565-9800579 chr12:9800682-9800693
24	TCF12	chr12:9800411-9801239	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:9800240-9801076	SK-N-MC	brain:	n/a	n/a
26	EP300	chr12:9800363-9802584	GM12878	blood:	n/a	chr12:9801950-9801964 chr12:9802375-9802389 chr12:9800672-9800688 chr12:9800673-9800689
27	JUND	chr12:9800471-9800990	A549	lung:	n/a	chr12:9800672-9800681
28	SIN3AK20	chr12:9800384-9801007	SK-N-SH	brain:	n/a	n/a
29	EP300	chr12:9800520-9802522	GM12878	blood:	n/a	chr12:9801950-9801964 chr12:9802375-9802389 chr12:9800672-9800688 chr12:9800673-9800689
30	ZC3H11A	chr12:9800831-9801006	K562	blood:	n/a	n/a
31	TBP	chr12:9800325-9800942	HepG2	liver:	n/a	n/a
32	POLR2A	chr12:9800075-9801532	U87	brain:	n/a	n/a
33	RUNX3	chr12:9799645-9802568	GM12878	blood:	n/a	chr12:9800805-9800822
34	BHLHE40	chr12:9800302-9801534	K562	blood:	n/a	chr12:9800672-9800688 chr12:9800678-9800694
35	POLR2A	chr12:9800194-9801236	HepG2	liver:	n/a	n/a
36	MYC	chr12:9800404-9801328	K562	blood:	n/a	n/a
37	POLR2A	chr12:9799501-9804451	GM12891	blood:	n/a	n/a
38	IRF1	chr12:9799891-9802485	K562	blood:	n/a	chr12:9801699-9801712 chr12:9802381-9802392 chr12:9801697-9801711 chr12:9802380-9802394 chr12:9800630-9800644 chr12:9801698-9801711 chr12:9801737-9801744 chr12:9801701-9801712 chr12:9801702-9801712 chr12:9801699-9801713 chr12:9801700-9801714 chr12:9801698-9801712 chr12:9801699-9801713
39	ZNF143	chr12:9800685-9801281	K562	blood:	n/a	chr12:9800829-9800838 chr12:9800827-9800845
40	KAP1	chr12:9799906-9802085	U2OS	brain:	n/a	chr12:9800521-9800529
41	CTBP2	chr12:9800343-9801323	H1-hESC	embryonic stem cell:	n/a	n/a
42	PAX5	chr12:9800590-9801177	GM12891	blood:	n/a	chr12:9800961-9800980
43	GTF2F1	chr12:9800341-9800946	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr12:9800322-9800958	A549	lung:	n/a	n/a
45	POLR2A	chr12:9799408-9804409	GM19099	blood:	n/a	n/a
46	E2F6	chr12:9800406-9800929	K562	blood:	n/a	chr12:9800667-9800678 chr12:9800668-9800680 chr12:9800566-9800576 chr12:9800777-9800792
47	TBP	chr12:9800754-9801174	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr12:9800366-9800970	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr12:9799796-9802695	HepG2	liver:	n/a	n/a
50	USF1	chr12:9800385-9800959	ECC-1	luminal epithelium:	n/a	chr12:9800672-9800688 chr12:9800678-9800694

No.	Distal block	Cell Line	Cell type
1	chr12:9799292..9802850-chr12:9823422..9827161,3	MCF-7	breast:
2	chr12:9739995..9741756-chr12:9800822..9803051,2	K562	blood:
3	chr12:9800923..9803675-chr12:9838767..9841892,3	MCF-7	breast:
4	chr12:9800782..9802831-chr12:9859086..9861954,2	MCF-7	breast:
5	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:
6	chr12:9800783..9805047-chr12:9809567..9813940,5	K562	blood:
7	chr12:9786143..9793024-chr12:9797652..9803573,13	MCF-7	breast:
8	chr12:9799537..9802341-chr12:9814175..9817797,3	K562	blood:
9	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC2D-8	chr12:9800643-9801529	NONHSAT026839
2	lnc-CLEC2D-8	chr12:9800643-9801529	NONHSAT026843
3	lnc-CLEC2D-8	chr12:9800698-9800972	NONHSAT026844

Variant related genes	Relation type
ENSG00000256442	TF binding region
ENSG00000069493	Chromatin interaction
ENSG00000256594	Chromatin interaction
ENSG00000257027	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10844269	0.81[AFR][1000 genomes]
rs2401386	0.80[ASN][1000 genomes]
rs3764023	0.88[AFR][1000 genomes]
rs7313927	0.85[AFR][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	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription 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	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7302081	LOC374443	cis	substantia nigra	BrainEAC
rs7302081	CLEC2D	cis	Nerve Tibial	GTEx
rs7302081	LOC374443	cis	intralobular white matter	BrainEAC
rs7302081	LOC374443	cis	hippocampus	BrainEAC
rs7302081	LOC374443	cis	brain	BrainEAC
rs7302081	LOC374443	cis	inferior olivary nucleus	BrainEAC

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9799800-9801400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:9799800-9801800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr12:9799800-9802200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:9799800-9803600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr12:9800000-9801000	Active TSS	Fetal Brain Female	brain
6	chr12:9800000-9801200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:9800000-9801800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr12:9800000-9801800	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr12:9800000-9802000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:9800000-9802000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:9800000-9802000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:9800000-9802200	Active TSS	Brain Germinal Matrix	brain
13	chr12:9800000-9802800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:9800000-9802800	Active TSS	Fetal Kidney	kidney
15	chr12:9800000-9803400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:9800000-9803600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:9800000-9804000	Active TSS	Rectal Smooth Muscle	rectum
18	chr12:9800200-9801000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:9800200-9801200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:9800200-9801200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr12:9800200-9801200	Flanking Active TSS	Dnd41	blood
22	chr12:9800200-9801400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:9800200-9801400	Flanking Active TSS	Liver	Liver
24	chr12:9800200-9801600	Active TSS	Gastric	stomach
25	chr12:9800200-9801800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr12:9800200-9801800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:9800200-9801800	Active TSS	A549	lung
28	chr12:9800200-9802000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr12:9800200-9802000	Active TSS	Fetal Intestine Small	intestine
30	chr12:9800200-9802000	Active TSS	Left Ventricle	heart
31	chr12:9800200-9802000	Active TSS	Psoas Muscle	Psoas
32	chr12:9800200-9802200	Active TSS	Aorta	Aorta
33	chr12:9800200-9802200	Active TSS	Brain Cingulate Gyrus	brain
34	chr12:9800200-9802200	Flanking Active TSS	HMEC	breast
35	chr12:9800200-9802400	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:9800200-9802400	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr12:9800200-9802400	Flanking Active TSS	HUVEC	blood vessel
38	chr12:9800200-9802600	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr12:9800200-9802600	Active TSS	Colon Smooth Muscle	Colon
40	chr12:9800200-9802600	Active TSS	Ovary	ovary
41	chr12:9800200-9802800	Active TSS	NHDF-Ad	bronchial
42	chr12:9800200-9803400	Active TSS	Brain Anterior Caudate	brain
43	chr12:9800200-9803400	Active TSS	Esophagus	oesophagus
44	chr12:9800200-9803400	Active TSS	Right Ventricle	heart
45	chr12:9800200-9803400	Active TSS	HSMMtube	muscle
46	chr12:9800200-9803600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:9800200-9804000	Active TSS	Right Atrium	heart
48	chr12:9800400-9801000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr12:9800400-9801200	Active TSS	Placenta Amnion	Placenta Amnion
50	chr12:9800400-9801400	Active TSS	iPS-18 Cell Line	embryonic stem cell

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