Variant report

Variant	rs2257156
Chromosome Location	chr12:105591083-105591084
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	POLR2A	chr12:105590936-105593428	A549	lung:	n/a	n/a
2	POLR2A	chr12:105590989-105593042	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:105590584-105592945	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:105590596-105593424	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:105590343-105591296	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr12:105591037-105591558	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:105590825-105593473	K562	blood:	n/a	n/a
8	POLR2A	chr12:105590525-105591402	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105589883..105591833-chr12:105596630..105599143,3	K562	blood:
2	chr12:105585594..105587866-chr12:105590129..105592324,2	MCF-7	breast:

Variant related genes	Relation type
APPL2	TF binding region

Extended variants
information (count: 143 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10746010	0.88[EUR][1000 genomes]
rs10778367	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs10778368	0.84[EUR][1000 genomes]
rs10778369	0.84[EUR][1000 genomes]
rs1078420	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1107755	0.84[EUR][1000 genomes]
rs1107757	0.84[EUR][1000 genomes]
rs11112424	0.84[EUR][1000 genomes]
rs11112434	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196742	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196745	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196748	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196749	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes]
rs1196753	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs1196754	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1196756	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1196764	0.97[EUR][1000 genomes]
rs1196765	0.96[EUR][1000 genomes]
rs1196770	0.92[EUR][1000 genomes]
rs1196772	0.92[EUR][1000 genomes]
rs1196777	0.91[EUR][1000 genomes]
rs1196780	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1196782	0.84[EUR][1000 genomes]
rs1196786	0.83[EUR][1000 genomes]
rs1196787	0.84[EUR][1000 genomes]
rs1196789	0.84[EUR][1000 genomes]
rs1196793	0.86[MEX][hapmap];0.84[EUR][1000 genomes]
rs1196795	0.85[CEU][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs1196797	0.85[CEU][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs1196798	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196800	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196801	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196805	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196806	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196807	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196808	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196811	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196813	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196817	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196819	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196820	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196823	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196825	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196831	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196833	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196834	0.81[EUR][1000 genomes]
rs1196839	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196841	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196842	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196844	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196847	0.85[EUR][1000 genomes]
rs1196848	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196851	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196853	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196859	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1196861	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196862	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196864	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196869	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196871	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1196872	0.82[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196873	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196874	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196881	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1196884	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1196885	0.83[EUR][1000 genomes]
rs1206559	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1209308	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1209637	0.85[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1211276	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1211277	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1211626	0.83[EUR][1000 genomes]
rs12309135	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12369709	0.82[EUR][1000 genomes]
rs12814458	0.84[EUR][1000 genomes]
rs12816560	0.84[EUR][1000 genomes]
rs1345096	0.88[EUR][1000 genomes]
rs1444610	0.84[EUR][1000 genomes]
rs1621553	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs1663565	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17036781	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1732370	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2166142	0.88[EUR][1000 genomes]
rs2246243	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2374449	1.00[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2440692	0.87[EUR][1000 genomes]
rs2440714	0.93[EUR][1000 genomes]
rs2440715	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs2440718	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2464173	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2464175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464181	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2464182	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35679386	0.83[EUR][1000 genomes]
rs4356312	0.82[EUR][1000 genomes]
rs4356313	0.90[EUR][1000 genomes]
rs4372534	0.87[EUR][1000 genomes]
rs4390426	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4964122	0.90[EUR][1000 genomes]
rs4964331	1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs57393988	0.94[ASN][1000 genomes]
rs57456392	0.94[ASN][1000 genomes]
rs60230439	0.94[ASN][1000 genomes]
rs60725801	0.94[ASN][1000 genomes]
rs61042175	0.87[ASN][1000 genomes]
rs6539183	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs6539186	0.83[EUR][1000 genomes]
rs6539187	0.84[EUR][1000 genomes]
rs6539188	0.87[EUR][1000 genomes]
rs7132040	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7132624	0.88[EUR][1000 genomes]
rs7132855	1.00[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs71441895	0.92[EUR][1000 genomes]
rs7299701	0.86[EUR][1000 genomes]
rs7302854	0.83[EUR][1000 genomes]
rs7303961	0.90[EUR][1000 genomes]
rs7307834	0.94[ASN][1000 genomes]
rs73181823	0.83[EUR][1000 genomes]
rs73395723	0.87[ASN][1000 genomes]
rs73395740	0.94[ASN][1000 genomes]
rs73395745	0.81[ASN][1000 genomes]
rs73395746	0.81[ASN][1000 genomes]
rs73395758	0.81[ASN][1000 genomes]
rs73395770	0.94[ASN][1000 genomes]
rs73395771	0.94[ASN][1000 genomes]
rs73395772	0.94[ASN][1000 genomes]
rs73395783	0.94[ASN][1000 genomes]
rs73395785	0.94[ASN][1000 genomes]
rs73397621	0.94[ASN][1000 genomes]
rs73397624	0.94[ASN][1000 genomes]
rs7963877	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs873119	0.86[EUR][1000 genomes]
rs935240	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs935241	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs935242	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs935244	0.85[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs935246	0.90[EUR][1000 genomes]
rs935248	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs935249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668528	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2257156	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL
rs2257156	APPL2	cis	cerebellum	SCAN
rs2257156	ALDH1L2	cis	cerebellum	SCAN
rs2257156	LOC387882	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105561400-105598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:105571400-105617800	Weak transcription	K562	blood
5	chr12:105576000-105593200	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr12:105576000-105595600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:105577200-105592200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:105577400-105592800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:105577400-105593600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:105577800-105591200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:105577800-105591400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:105577800-105592200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:105577800-105592600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:105577800-105593400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:105577800-105594200	Strong transcription	Fetal Intestine Large	intestine
19	chr12:105577800-105594400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:105577800-105595200	Strong transcription	Left Ventricle	heart
21	chr12:105577800-105598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:105577800-105598800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr12:105577800-105599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:105577800-105602600	Strong transcription	Fetal Thymus	thymus
25	chr12:105577800-105603600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
28	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr12:105578000-105593000	Strong transcription	Osteobl	bone
30	chr12:105578000-105593400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:105578000-105593400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:105578000-105599200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr12:105578000-105607400	Strong transcription	Fetal Brain Female	brain
34	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:105578200-105593600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr12:105578400-105593400	Strong transcription	NHLF	lung
38	chr12:105578400-105602400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:105578800-105592800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:105579000-105593000	Strong transcription	NHEK	skin
41	chr12:105579000-105598600	Strong transcription	HSMM	muscle
42	chr12:105579000-105605200	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:105579000-105612400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr12:105579200-105593400	Strong transcription	Placenta	Placenta
45	chr12:105579400-105593000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:105579400-105595000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:105579800-105593000	Strong transcription	Fetal Lung	lung
48	chr12:105579800-105596000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:105580200-105613200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:105581200-105602600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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