Variant report

Variant	rs1201657
Chromosome Location	chr12:105587475-105587476
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	chr12:105587120-105588070	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:105587309-105587495	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:105587430-105587602	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105585594..105587866-chr12:105590129..105592324,2	MCF-7	breast:
2	chr12:105586360..105589934-chr12:105601343..105605180,3	MCF-7	breast:

Variant related genes	Relation type
APPL2	TF binding region
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10861327	0.85[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs10861328	0.85[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs10861329	0.85[CEU][hapmap]
rs10861330	0.85[CEU][hapmap]
rs10861335	0.85[CEU][hapmap]
rs10861336	0.85[CEU][hapmap]
rs1109432	0.93[EUR][1000 genomes]
rs11112347	0.85[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs11112350	0.85[CEU][hapmap]
rs11112351	0.85[CEU][hapmap]
rs11112414	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11612252	0.85[CEU][hapmap]
rs11613261	0.85[CEU][hapmap]
rs1196750	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196752	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1196758	0.96[CEU][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1196766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1196767	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1196768	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes]
rs1196776	0.93[EUR][1000 genomes]
rs1196778	0.93[EUR][1000 genomes]
rs1196779	0.91[EUR][1000 genomes]
rs1196781	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs1196785	0.86[EUR][1000 genomes]
rs1196788	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs1196796	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs1196803	0.94[ASN][1000 genomes]
rs1196804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196809	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196810	0.93[ASN][1000 genomes]
rs1196812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1196814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1196821	0.89[ASN][1000 genomes]
rs1196822	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1196826	0.92[ASN][1000 genomes]
rs1196827	0.92[ASN][1000 genomes]
rs1196828	0.92[ASN][1000 genomes]
rs1196829	0.92[ASN][1000 genomes]
rs1196835	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1196836	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1196837	0.90[ASN][1000 genomes]
rs1196838	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1196840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1196843	0.87[ASN][1000 genomes]
rs1196846	0.91[ASN][1000 genomes]
rs1196850	0.89[ASN][1000 genomes]
rs1196854	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196855	0.94[ASN][1000 genomes]
rs1196856	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196858	0.97[ASN][1000 genomes]
rs1196860	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196865	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196866	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196867	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196868	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196870	0.94[ASN][1000 genomes]
rs1196876	0.94[ASN][1000 genomes]
rs1196877	0.94[ASN][1000 genomes]
rs1196878	0.96[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196880	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196882	0.89[CEU][hapmap]
rs1196883	0.86[CHD][hapmap]
rs1201658	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12581638	0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs17036869	0.85[CHB][hapmap]
rs1732371	0.88[ASN][1000 genomes]
rs1732377	0.80[EUR][1000 genomes]
rs1732378	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1732379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732384	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2246510	0.96[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2264066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2374448	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2440693	0.80[EUR][1000 genomes]
rs2440708	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs2440713	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2440717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2440719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4144468	0.85[CEU][hapmap]
rs4964127	0.86[EUR][1000 genomes]
rs4964346	0.84[EUR][1000 genomes]
rs6539196	0.85[EUR][1000 genomes]
rs727888	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs7308195	0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs7309320	0.85[EUR][1000 genomes]
rs7310488	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs7969800	0.85[EUR][1000 genomes]
rs9143	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv870352	chr12:105557770-105589263	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	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
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1201657	APPL2	cis	cerebellum	SCAN
rs1201657	ALDH1L2	cis	cerebellum	SCAN
rs1201657	APPL2	cis	Whole Blood	GTEx

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	chr12:105568000-105589400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:105571400-105617800	Weak transcription	K562	blood
6	chr12:105576000-105593200	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr12:105576000-105595600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:105577200-105589400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:105577200-105592200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:105577400-105592800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:105577400-105593600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:105577600-105589200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:105577800-105589600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr12:105577800-105591200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:105577800-105591400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr12:105577800-105592200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:105577800-105592600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:105577800-105593400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:105577800-105594200	Strong transcription	Fetal Intestine Large	intestine
23	chr12:105577800-105594400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:105577800-105595200	Strong transcription	Left Ventricle	heart
25	chr12:105577800-105598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:105577800-105598800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:105577800-105599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:105577800-105602600	Strong transcription	Fetal Thymus	thymus
29	chr12:105577800-105603600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
32	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:105578000-105588600	Strong transcription	Liver	Liver
34	chr12:105578000-105589400	Strong transcription	Primary T cells from cord blood	blood
35	chr12:105578000-105589400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:105578000-105590800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:105578000-105593000	Strong transcription	Osteobl	bone
38	chr12:105578000-105593400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:105578000-105593400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:105578000-105599200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr12:105578000-105607400	Strong transcription	Fetal Brain Female	brain
42	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:105578200-105589400	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr12:105578200-105593600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:105578400-105593400	Strong transcription	NHLF	lung
47	chr12:105578400-105602400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:105578800-105592800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:105579000-105589600	Strong transcription	NH-A	brain
50	chr12:105579000-105593000	Strong transcription	NHEK	skin

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