Variant report

Variant	rs12813695
Chromosome Location	chr12:31905730-31905731
allele	G/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	POLR2A	chr12:31904965-31905780	GM12878	blood:	n/a	n/a
2	RCOR1	chr12:31904843-31905840	GM12878	blood:	n/a	n/a
3	EBF1	chr12:31905259-31905832	GM12878	blood:	n/a	n/a
4	ZNF384	chr12:31904717-31905957	GM12878	blood:	n/a	n/a
5	CUX1	chr12:31905302-31905839	GM12878	blood:	n/a	n/a
6	MXI1	chr12:31905080-31905832	GM12878	blood:	n/a	n/a
7	TBP	chr12:31904964-31905733	GM12878	blood:	n/a	n/a
8	ESRRA	chr12:31902945-31906220	GM12878	blood:	n/a	chr12:31905114-31905124 chr12:31905112-31905124 chr12:31905112-31905125 chr12:31905114-31905124
9	EP300	chr12:31905520-31905835	GM12878	blood:	n/a	n/a
10	MAX	chr12:31904912-31905792	GM12878	blood:	n/a	n/a
11	MAZ	chr12:31905077-31905743	GM12878	blood:	n/a	n/a
12	EP300	chr12:31905474-31905761	K562	blood:	n/a	n/a
13	NFIC	chr12:31904716-31905769	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31900170..31902250-chr12:31904037..31906770,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256843	TF binding region
ENSG00000223722	TF binding region
ENSG00000256843	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10844000	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[YRI][hapmap]
rs10844002	0.90[ASN][1000 genomes]
rs10844003	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844047	1.00[YRI][hapmap]
rs11051525	0.80[AMR][1000 genomes]
rs11051541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs11051545	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs11051555	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11051559	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367895	0.80[AMR][1000 genomes]
rs12813042	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs12813399	0.80[AMR][1000 genomes]
rs4272861	1.00[CHB][hapmap]
rs7297921	0.80[AMR][1000 genomes]
rs7300260	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs7953551	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs7969019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7970737	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	esv2422415	chr12:31863360-31930722	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv558100	chr12:31866833-32185924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1045464	chr12:31869888-32183792	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv541447	chr12:31869888-32183792	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
13	nsv558101	chr12:31876666-32006563	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv1050448	chr12:31877289-31927006	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv558102	chr12:31889824-31907409	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv975473	chr12:31895430-31908180	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv8940	chr12:31899904-31987363	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
18	nsv442261	chr12:31900550-31909906	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	esv2421936	chr12:31900550-31909908	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	esv2760910	chr12:31900550-31909908	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv558103	chr12:31900550-31909908	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv558104	chr12:31900550-31910908	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv558105	chr12:31900550-31912588	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv558106	chr12:31900550-31914143	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv558107	chr12:31900550-31919188	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	esv1836353	chr12:31903771-31912588	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	esv1841335	chr12:31903771-31912588	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	nsv818904	chr12:31903771-31912588	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
29	nsv515490	chr12:31903771-31919188	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	esv11695	chr12:31904381-31911808	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	esv3327147	chr12:31905485-31913483	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12813695	C12orf72	cis	cerebellum	SCAN
rs12813695	AMN1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31889400-31905800	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:31893600-31905800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:31900000-31905800	Enhancers	Primary B cells from cord blood	blood
4	chr12:31900000-31906400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:31901000-31909800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:31901800-31905800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:31902600-31906400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr12:31902600-31908600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:31902600-31908600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:31902600-31912800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:31903600-31912800	Weak transcription	Gastric	stomach
12	chr12:31903800-31905800	Weak transcription	Right Atrium	heart
13	chr12:31903800-31909800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:31904000-31909600	Weak transcription	HMEC	breast
15	chr12:31904200-31908400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:31904200-31909600	Weak transcription	Hela-S3	cervix
17	chr12:31904200-31909800	Weak transcription	Small Intestine	intestine
18	chr12:31904200-31909800	Weak transcription	Stomach Mucosa	stomach
19	chr12:31904400-31905800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:31904400-31905800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:31904600-31908400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:31904800-31909800	Weak transcription	HUVEC	blood vessel
23	chr12:31905000-31909800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:31905200-31905800	Enhancers	H9 Cell Line	embryonic stem cell
25	chr12:31905200-31905800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr12:31905200-31905800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:31905200-31905800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:31905200-31905800	Enhancers	HSMMtube	muscle
29	chr12:31905400-31905800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr12:31905400-31909800	Weak transcription	Placenta	Placenta
31	chr12:31905400-31912200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:31905400-31912800	Weak transcription	HepG2	liver
33	chr12:31905600-31905800	Enhancers	GM12878-XiMat	blood
34	chr12:31905600-31906400	Enhancers	Dnd41	blood
35	chr12:31905600-31907800	Weak transcription	Spleen	Spleen
36	chr12:31905600-31908400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:31905600-31908400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:31905600-31908600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:31905600-31909600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:31905600-31909600	Weak transcription	A549	lung
41	chr12:31905600-31909800	Weak transcription	K562	blood

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