Variant report

Variant	rs7975716
Chromosome Location	chr12:9804181-9804182
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	POLR2A	chr12:9799451-9804403	GM19193	blood:	n/a	n/a
2	MAX	chr12:9803994-9804287	K562	blood:	n/a	n/a
3	SPI1	chr12:9803915-9804357	HL-60	blood:	n/a	n/a
4	MTA3	chr12:9799406-9804477	GM12878	blood:	n/a	n/a
5	TBP	chr12:9803954-9804332	K562	blood:	n/a	n/a
6	MYC	chr12:9802783-9804371	NB4	blood:	n/a	chr12:9803552-9803562
7	MAX	chr12:9802772-9804331	NB4	blood:	n/a	chr12:9803552-9803562
8	RCOR1	chr12:9803270-9804348	GM12878	blood:	n/a	n/a
9	RELA	chr12:9803312-9804472	GM18526	blood:	n/a	n/a
10	MAX	chr12:9803341-9804341	GM12878	blood:	n/a	chr12:9803552-9803562
11	POLR2A	chr12:9799501-9804451	GM12891	blood:	n/a	n/a
12	YY1	chr12:9804013-9804270	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:9799408-9804409	GM19099	blood:	n/a	n/a
14	SPI1	chr12:9804062-9804263	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:9799328-9804610	GM12878	blood:	n/a	n/a
16	ATF2	chr12:9800087-9804473	GM12878	blood:	n/a	n/a
17	FOXM1	chr12:9803060-9804211	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:9800142-9804355	GM18951	blood:	n/a	n/a
19	CBX3	chr12:9803724-9804484	K562	blood:	n/a	n/a
20	POLR2A	chr12:9799314-9804469	GM12892	blood:	n/a	n/a
21	SPI1	chr12:9803976-9804268	K562	blood:	n/a	n/a
22	MYC	chr12:9802846-9804368	K562	blood:	n/a	chr12:9803552-9803562
23	JUND	chr12:9803374-9804276	K562	blood:	n/a	n/a
24	EP300	chr12:9803289-9804338	GM12878	blood:	n/a	chr12:9803464-9803478 chr12:9803460-9803469
25	NFIC	chr12:9799779-9804349	GM12878	blood:	n/a	n/a
26	TBP	chr12:9803278-9804346	GM12878	blood:	n/a	n/a
27	RELA	chr12:9803258-9804469	GM10847	blood:	n/a	n/a
28	POLR2A	chr12:9799501-9804422	GM18526	blood:	n/a	n/a
29	MXI1	chr12:9803283-9804288	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:9799475-9804347	GM12892	blood:	n/a	n/a
31	POLR2A	chr12:9799681-9804387	Raji	blood:	n/a	n/a
32	SPI1	chr12:9804002-9804277	K562	blood:	n/a	n/a
33	MAZ	chr12:9803291-9804284	GM12878	blood:	n/a	n/a
34	RELA	chr12:9799625-9804451	GM19193	blood:	n/a	n/a
35	RELA	chr12:9799837-9804323	GM18505	blood:	n/a	n/a
36	TAF1	chr12:9804060-9804293	K562	blood:	n/a	n/a
37	GATA2	chr12:9804121-9804421	K562	blood:	n/a	n/a
38	ZNF143	chr12:9803924-9804395	K562	blood:	n/a	n/a
39	POLR2A	chr12:9804002-9804382	K562	blood:	n/a	n/a
40	RUNX3	chr12:9803209-9804465	GM12878	blood:	n/a	chr12:9803476-9803491
41	MTA3	chr12:9803869-9804581	GM12878	blood:	n/a	n/a
42	WRNIP1	chr12:9804161-9804361	GM12878	blood:	n/a	n/a
43	RELA	chr12:9799841-9804488	GM18951	blood:	n/a	n/a
44	POLR2A	chr12:9799520-9804579	GM12878	blood:	n/a	n/a
45	NFIC	chr12:9803053-9804359	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:9799517-9804360	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:9803951-9804324	GM12878	blood:	n/a	n/a
48	RUNX3	chr12:9802733-9804441	GM12878	blood:	n/a	chr12:9803476-9803491
49	ELF1	chr12:9803906-9804393	GM12878	blood:	n/a	chr12:9804144-9804157
50	POLR2A	chr12:9799348-9804458	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:
2	chr12:9802928..9804462-chr12:9806298..9808980,2	K562	blood:
3	chr12:9800783..9805047-chr12:9809567..9813940,5	K562	blood:
4	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:

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

Extended variants
information (count: 47 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10047657	0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10771987	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10772001	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10772005	0.83[LWK][hapmap];0.80[YRI][hapmap]
rs10772006	0.83[LWK][hapmap];0.80[YRI][hapmap]
rs10772010	0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10844325	0.91[ASN][1000 genomes]
rs10844350	0.80[YRI][hapmap]
rs10844351	0.80[YRI][hapmap]
rs10844359	0.80[YRI][hapmap]
rs10844373	0.91[ASN][1000 genomes]
rs11052274	0.89[YRI][hapmap]
rs1560007	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs16913477	0.82[LWK][hapmap];0.80[YRI][hapmap]
rs17805558	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1863873	0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1863874	0.91[ASN][1000 genomes]
rs2114869	0.80[YRI][hapmap]
rs34383380	0.91[ASN][1000 genomes]
rs3764023	0.89[ASN][1000 genomes]
rs3764024	0.89[ASN][1000 genomes]
rs7131784	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7132037	0.80[YRI][hapmap]
rs7299076	0.96[ASN][1000 genomes]
rs7302746	0.80[YRI][hapmap]
rs7304464	0.80[YRI][hapmap]
rs7309800	0.80[YRI][hapmap]
rs7310568	0.84[LWK][hapmap];0.80[YRI][hapmap]
rs7310790	0.80[LWK][hapmap];0.80[YRI][hapmap]
rs7311421	0.84[YRI][hapmap]
rs7311574	0.80[YRI][hapmap]
rs7313927	0.90[ASN][1000 genomes]
rs7316121	0.97[ASN][1000 genomes]
rs7959272	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7962321	0.82[LWK][hapmap];0.80[YRI][hapmap]
rs7974871	0.83[LWK][hapmap];0.80[YRI][hapmap]
rs7978187	0.80[YRI][hapmap]
rs969367	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9919786	0.84[LWK][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7975716	AICDA	cis	parietal	SCAN
rs7975716	DDX12	cis	lymphoblastoid	seeQTL
rs7975716	CLEC1A	cis	parietal	SCAN
rs7975716	LOC642846	cis	lymphoblastoid	seeQTL
rs7975716	CLEC2D	cis	multi-tissue	Pritchard
rs7975716	DCAL1	cis	multi-tissue	Pritchard
rs7975716	CLEC2D	cis	cerebellum	SCAN
rs7975716	CLEC2A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9800600-9804200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:9801000-9804400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr12:9801200-9804400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:9801400-9804400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:9801600-9804200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:9801600-9804200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr12:9801600-9811200	Weak transcription	Gastric	stomach
8	chr12:9801600-9815600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:9801800-9804400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:9802000-9805200	Flanking Active TSS	Dnd41	blood
11	chr12:9802200-9804400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr12:9802200-9806600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:9802200-9815200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:9802400-9804400	Enhancers	HUVEC	blood vessel
15	chr12:9802400-9806200	Weak transcription	A549	lung
16	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
17	chr12:9802600-9804200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:9802600-9807200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:9802600-9812800	Weak transcription	Ovary	ovary
20	chr12:9802600-9814400	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:9802800-9804400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr12:9803000-9804200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr12:9803000-9804200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:9803000-9804200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:9803000-9804600	Flanking Active TSS	GM12878-XiMat	blood
26	chr12:9803000-9805000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:9803000-9806000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:9803000-9806600	Weak transcription	Placenta	Placenta
29	chr12:9803000-9806600	Weak transcription	Psoas Muscle	Psoas
30	chr12:9803000-9811200	Weak transcription	Fetal Intestine Small	intestine
31	chr12:9803000-9812200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:9803000-9816400	Weak transcription	Brain Germinal Matrix	brain
33	chr12:9803000-9816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
35	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
36	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
37	chr12:9803200-9804200	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr12:9803200-9804200	Enhancers	NH-A	brain
39	chr12:9803200-9804400	Enhancers	Fetal Brain Male	brain
40	chr12:9803200-9804400	Enhancers	NHDF-Ad	bronchial
41	chr12:9803200-9812400	Weak transcription	Liver	Liver
42	chr12:9803200-9813400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:9803400-9804200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:9803400-9804200	Enhancers	Right Ventricle	heart
45	chr12:9803400-9804200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr12:9803400-9804400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:9803400-9804400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:9803400-9804400	Flanking Active TSS	Fetal Thymus	thymus
49	chr12:9803400-9804400	Enhancers	Left Ventricle	heart
50	chr12:9803400-9804600	Enhancers	HMEC	breast

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