Variant report

Variant	rs12231666
Chromosome Location	chr12:31868968-31868969
allele	A/C
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	chr12:31867829-31869556	K562	blood:	n/a	n/a
2	GATA1	chr12:31868001-31869193	PBDE	blood:	n/a	chr12:31868338-31868347 chr12:31868339-31868356 chr12:31868275-31868282
3	ZC3H11A	chr12:31868146-31869046	K562	blood:	n/a	n/a
4	JUN	chr12:31868042-31869483	K562	blood:	n/a	n/a
5	MAFF	chr12:31868099-31869914	K562	blood:	n/a	n/a
6	CUX1	chr12:31867772-31869456	K562	blood:	n/a	n/a
7	POLR2A	chr12:31868061-31868984	K562	blood:	n/a	n/a
8	POLR2A	chr12:31867588-31869074	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:31868050-31869745	K562	blood:	n/a	n/a
10	IRF1	chr12:31867498-31870010	K562	blood:	n/a	chr12:31868419-31868433 chr12:31868097-31868111 chr12:31868097-31868110 chr12:31868419-31868430 chr12:31868097-31868110 chr12:31868890-31868903 chr12:31868417-31868431 chr12:31868098-31868108 chr12:31868097-31868110 chr12:31868098-31868112 chr12:31868418-31868432
11	TAL1	chr12:31868007-31869727	K562	blood:	n/a	n/a
12	EP300	chr12:31867940-31869748	K562	blood:	n/a	chr12:31868422-31868436
13	POLR2A	chr12:31868065-31869541	K562	blood:	n/a	n/a
14	POLR2A	chr12:31867932-31870478	K562	blood:	n/a	n/a
15	POLR2A	chr12:31868956-31869454	K562	blood:	n/a	n/a
16	ARID3A	chr12:31867921-31869074	K562	blood:	n/a	n/a
17	TBL1XR1	chr12:31867855-31869895	K562	blood:	n/a	n/a
18	IRF1	chr12:31867576-31869751	K562	blood:	n/a	chr12:31868419-31868433 chr12:31868097-31868111 chr12:31868097-31868110 chr12:31868419-31868430 chr12:31868097-31868110 chr12:31868890-31868903 chr12:31868417-31868431 chr12:31868098-31868108 chr12:31868097-31868110 chr12:31868098-31868112 chr12:31868418-31868432
19	EP300	chr12:31868008-31869032	GM12878	blood:	n/a	chr12:31868422-31868436
20	TBP	chr12:31868058-31869482	K562	blood:	n/a	n/a
21	BCLAF1	chr12:31868020-31869037	K562	blood:	n/a	chr12:31868099-31868108
22	EP300	chr12:31868153-31869283	K562	blood:	n/a	chr12:31868422-31868436
23	MYC	chr12:31868010-31869113	K562	blood:	n/a	n/a
24	ZMIZ1	chr12:31868136-31869419	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31811076..31814149-chr12:31866420..31869336,3	K562	blood:
2	chr12:31867508..31869786-chr12:31900848..31903323,2	K562	blood:
3	chr12:31868001..31870341-chr12:32112733..32115276,2	K562	blood:
4	chr12:31866804..31870237-chr12:31900678..31903673,4	K562	blood:

Variant related genes	Relation type
AMN1	TF binding region
ENSG00000256843	Chromatin interaction
ENSG00000139160	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10843992	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11051514	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11051515	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11051516	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11051517	0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs11051519	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051522	0.92[MEX][hapmap]
rs11051527	0.90[ASN][1000 genomes]
rs11051534	0.90[ASN][1000 genomes]
rs11051535	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11051536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11051537	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11051538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11051540	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11051546	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11051547	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11051549	0.96[AMR][1000 genomes]
rs11051551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes]
rs4931536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4931538	0.90[ASN][1000 genomes]
rs4931545	0.91[ASN][1000 genomes]
rs4931546	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4931547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59091295	0.98[ASN][1000 genomes]
rs61932065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61932089	0.94[AMR][1000 genomes]
rs7308889	0.86[ASN][1000 genomes]
rs7959989	0.84[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	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	nsv898967	chr12:31858031-31899475	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12231666	BICD1	cis	cerebellum	SCAN
rs12231666	REP15	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31822600-31874200	Weak transcription	Right Ventricle	heart
2	chr12:31827000-31871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:31838600-31881000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:31839800-31871800	Weak transcription	Gastric	stomach
5	chr12:31841600-31870000	Weak transcription	Pancreas	Pancrea
6	chr12:31844600-31871800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:31846400-31871800	Weak transcription	Lung	lung
8	chr12:31849000-31880000	Weak transcription	Psoas Muscle	Psoas
9	chr12:31851000-31880800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:31852800-31871000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:31852800-31879600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:31859000-31871800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:31860400-31872400	Weak transcription	Fetal Kidney	kidney
14	chr12:31860600-31874000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:31860800-31871800	Weak transcription	Ovary	ovary
16	chr12:31860800-31881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:31861000-31871800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:31862200-31880600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:31862400-31871800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:31862600-31871200	Weak transcription	Fetal Lung	lung
21	chr12:31862600-31871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:31862800-31871800	Weak transcription	Aorta	Aorta
23	chr12:31862800-31874200	Weak transcription	Left Ventricle	heart
24	chr12:31864000-31871800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:31865400-31871800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:31866600-31871600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:31867600-31871800	Weak transcription	Spleen	Spleen
28	chr12:31867800-31869200	Flanking Active TSS	GM12878-XiMat	blood
29	chr12:31867800-31869800	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr12:31868000-31869000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:31868200-31869000	Enhancers	Brain Hippocampus Middle	brain
32	chr12:31868200-31870600	Active TSS	K562	blood
33	chr12:31868200-31871800	Weak transcription	Fetal Intestine Large	intestine
34	chr12:31868400-31869000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr12:31868400-31869000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:31868400-31869400	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr12:31868400-31879600	Weak transcription	Brain Angular Gyrus	brain
38	chr12:31868600-31869000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:31868600-31869800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr12:31868600-31871600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:31868600-31871800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:31868600-31871800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:31868600-31874200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:31868600-31875200	Weak transcription	A549	lung
45	chr12:31868800-31869000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:31868800-31869000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:31868800-31869000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr12:31868800-31869000	Weak transcription	Stomach Mucosa	stomach
49	chr12:31868800-31869200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:31868800-31869200	Enhancers	HepG2	liver

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