Variant report

Variant	rs1560007
Chromosome Location	chr12:9802531-9802532
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	MXI1	chr12:9800287-9802771	GM12878	blood:	n/a	n/a
2	CHD1	chr12:9800337-9804156	GM12878	blood:	n/a	chr12:9800667-9800677 chr12:9800660-9800670
3	TBL1XR1	chr12:9799984-9802966	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:9799451-9804403	GM19193	blood:	n/a	n/a
5	MTA3	chr12:9799406-9804477	GM12878	blood:	n/a	n/a
6	EP300	chr12:9800363-9802584	GM12878	blood:	n/a	chr12:9801950-9801964 chr12:9802375-9802389 chr12:9800672-9800688 chr12:9800673-9800689
7	EBF1	chr12:9801511-9802586	GM12878	blood:	n/a	chr12:9802311-9802322
8	RUNX3	chr12:9801803-9802561	GM12878	blood:	n/a	n/a
9	RUNX3	chr12:9799645-9802568	GM12878	blood:	n/a	chr12:9800805-9800822
10	POLR2A	chr12:9799501-9804451	GM12891	blood:	n/a	n/a
11	MYC	chr12:9801820-9803973	MCF10A-Er-Src	breast:	n/a	chr12:9803552-9803562
12	POLR2A	chr12:9799408-9804409	GM19099	blood:	n/a	n/a
13	POLR2A	chr12:9799796-9802695	HepG2	liver:	n/a	n/a
14	TBP	chr12:9802082-9802946	GM12878	blood:	n/a	n/a
15	UBTF	chr12:9801914-9802802	K562	blood:	n/a	n/a
16	POLR2A	chr12:9799328-9804610	GM12878	blood:	n/a	n/a
17	ATF2	chr12:9800087-9804473	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:9801852-9802533	GM12891	blood:	n/a	n/a
19	POLR2A	chr12:9800142-9804355	GM18951	blood:	n/a	n/a
20	POLR2A	chr12:9799314-9804469	GM12892	blood:	n/a	n/a
21	POLR2A	chr12:9799782-9803691	NB4	blood:	n/a	n/a
22	NFIC	chr12:9799779-9804349	GM12878	blood:	n/a	n/a
23	SPI1	chr12:9802187-9802602	GM12891	blood:	n/a	n/a
24	POLR2A	chr12:9799501-9804422	GM18526	blood:	n/a	n/a
25	STAT5A	chr12:9799903-9804021	GM12878	blood:	n/a	chr12:9800489-9800496 chr12:9801700-9801711 chr12:9803497-9803505 chr12:9800768-9800780
26	POLR2A	chr12:9799475-9804347	GM12892	blood:	n/a	n/a
27	RELA	chr12:9800358-9802939	GM18526	blood:	n/a	n/a
28	POLR2A	chr12:9799681-9804387	Raji	blood:	n/a	n/a
29	NFIC	chr12:9800239-9802953	GM12878	blood:	n/a	n/a
30	RELA	chr12:9799625-9804451	GM19193	blood:	n/a	n/a
31	SPI1	chr12:9802033-9802572	GM12878	blood:	n/a	n/a
32	CUX1	chr12:9800331-9802732	GM12878	blood:	n/a	n/a
33	RELA	chr12:9799837-9804323	GM18505	blood:	n/a	n/a
34	POLR2A	chr12:9802455-9802787	K562	blood:	n/a	n/a
35	POLR2A	chr12:9800204-9803221	HL-60	blood:	n/a	n/a
36	BCLAF1	chr12:9799795-9803076	GM12878	blood:	n/a	chr12:9800683-9800696 chr12:9800565-9800578
37	RELA	chr12:9799841-9804488	GM18951	blood:	n/a	n/a
38	POLR2A	chr12:9799734-9803978	MCF10A-Er-Src	breast:	n/a	n/a
39	BHLHE40	chr12:9800203-9802559	GM12878	blood:	n/a	chr12:9800672-9800688 chr12:9800678-9800694
40	POLR2A	chr12:9799520-9804579	GM12878	blood:	n/a	n/a
41	POLR2A	chr12:9799517-9804360	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:9799348-9804458	GM12892	blood:	n/a	n/a
43	FOXM1	chr12:9800133-9802549	GM12878	blood:	n/a	n/a
44	POLR2A	chr12:9800379-9802983	GM10847	blood:	n/a	n/a
45	NFATC1	chr12:9800289-9802642	GM12878	blood:	n/a	n/a
46	ATF2	chr12:9802124-9802733	GM12878	blood:	n/a	n/a
47	FOXM1	chr12:9801921-9802932	GM12878	blood:	n/a	n/a
48	POLR2A	chr12:9802017-9802561	HepG2	liver:	n/a	n/a
49	PML	chr12:9800165-9804429	GM12878	blood:	n/a	chr12:9800521-9800529 chr12:9802383-9802391
50	STAT5A	chr12:9801726-9802606	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9801129..9802680-chr12:9843178..9846016,2	K562	blood:
2	chr12:9801303..9803979-chr12:9875830..9877610,2	K562	blood:
3	chr12:9799292..9802850-chr12:9823422..9827161,3	MCF-7	breast:
4	chr12:9801031..9803712-chr12:9946954..9949811,3	K562	blood:
5	chr12:9739995..9741756-chr12:9800822..9803051,2	K562	blood:
6	chr12:9800923..9803675-chr12:9838767..9841892,3	MCF-7	breast:
7	chr12:9800782..9802831-chr12:9859086..9861954,2	MCF-7	breast:
8	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:
9	chr12:9600285..9602561-chr12:9801026..9803503,2	K562	blood:
10	chr12:9800783..9805047-chr12:9809567..9813940,5	K562	blood:
11	chr12:9786143..9793024-chr12:9797652..9803573,13	MCF-7	breast:
12	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256594	TF binding region
ENSG00000256442	TF binding region
ENSG00000069493	Chromatin interaction
ENSG00000256594	Chromatin interaction
ENSG00000214826	Chromatin interaction
ENSG00000257027	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10047657	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10734805	0.86[YRI][hapmap]
rs10771987	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772001	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10772010	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10844325	0.92[ASN][1000 genomes]
rs10844373	0.92[ASN][1000 genomes]
rs1108452	0.86[YRI][hapmap]
rs1108453	0.95[LWK][hapmap];0.86[YRI][hapmap]
rs17805558	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1863873	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1863874	0.92[ASN][1000 genomes]
rs34383380	0.92[ASN][1000 genomes]
rs3764023	0.93[ASN][1000 genomes]
rs3764024	0.93[ASN][1000 genomes]
rs4439599	0.95[LWK][hapmap];0.86[YRI][hapmap]
rs4763716	0.80[AMR][1000 genomes]
rs6488100	0.86[YRI][hapmap]
rs7131784	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72656629	0.80[AMR][1000 genomes]
rs7299076	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306991	0.86[YRI][hapmap]
rs7313927	0.94[ASN][1000 genomes]
rs7316121	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959272	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7975716	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs969367	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1560007	CLEC2D	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9799800-9803600	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:9800000-9802800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:9800000-9802800	Active TSS	Fetal Kidney	kidney
4	chr12:9800000-9803400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:9800000-9803600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:9800000-9804000	Active TSS	Rectal Smooth Muscle	rectum
7	chr12:9800200-9802600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:9800200-9802600	Active TSS	Colon Smooth Muscle	Colon
9	chr12:9800200-9802600	Active TSS	Ovary	ovary
10	chr12:9800200-9802800	Active TSS	NHDF-Ad	bronchial
11	chr12:9800200-9803400	Active TSS	Brain Anterior Caudate	brain
12	chr12:9800200-9803400	Active TSS	Esophagus	oesophagus
13	chr12:9800200-9803400	Active TSS	Right Ventricle	heart
14	chr12:9800200-9803400	Active TSS	HSMMtube	muscle
15	chr12:9800200-9803600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:9800200-9804000	Active TSS	Right Atrium	heart
17	chr12:9800400-9802800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:9800400-9802800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:9800400-9803200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:9800400-9803400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:9800400-9803400	Active TSS	Brain Hippocampus Middle	brain
22	chr12:9800400-9803600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:9800400-9803600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr12:9800400-9803600	Active TSS	K562	blood
25	chr12:9800400-9803800	Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr12:9800600-9802800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:9800600-9802800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:9800600-9802800	Active TSS	HSMM	muscle
29	chr12:9800600-9803000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:9800600-9803000	Active TSS	Primary B cells from peripheral blood	blood
31	chr12:9800600-9803000	Active TSS	Stomach Smooth Muscle	stomach
32	chr12:9800600-9803000	Active TSS	GM12878-XiMat	blood
33	chr12:9800600-9803400	Active TSS	Colonic Mucosa	Colon
34	chr12:9800600-9803400	Active TSS	Fetal Thymus	thymus
35	chr12:9800600-9803400	Active TSS	NHLF	lung
36	chr12:9800600-9803600	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr12:9800600-9803600	Active TSS	Primary T cells from cord blood	blood
38	chr12:9800600-9803600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:9800600-9803600	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr12:9800600-9803600	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr12:9800600-9803600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:9800600-9803600	Active TSS	Thymus	Thymus
43	chr12:9800600-9803600	Active TSS	Monocytes-CD14+_RO01746	blood
44	chr12:9800600-9803800	Active TSS	Primary T cells fromperipheralblood	blood
45	chr12:9800600-9803800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:9800600-9804000	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr12:9800600-9804200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:9800800-9803800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:9801000-9803000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr12:9801000-9803200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood

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