Variant report

Variant	rs1196781
Chromosome Location	chr12:105627084-105627085
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	NR3C1	chr12:105626791-105627134	A549	lung:	n/a	n/a
2	POLR2A	chr12:105627030-105627206	ProgFib	skin:	n/a	n/a
3	NR3C1	chr12:105626702-105627117	A549	lung:	n/a	chr12:105626749-105626763
4	NR3C1	chr12:105626704-105627212	A549	lung:	n/a	chr12:105626749-105626763

No.	Distal block	Cell Line	Cell type
1	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:
2	chr12:105599435..105602379-chr12:105626303..105628956,2	K562	blood:
3	chr12:105620755..105625323-chr12:105625745..105629848,5	K562	blood:
4	chr12:105609511..105612358-chr12:105625566..105629291,3	K562	blood:

Variant related genes	Relation type
APPL2	TF binding region
C12orf75	TF binding region
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10778374	0.81[ASN][1000 genomes]
rs10778375	0.85[ASN][1000 genomes]
rs10861327	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs10861328	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs10861329	0.85[CEU][hapmap]
rs10861330	0.85[CEU][hapmap]
rs10861335	0.85[CEU][hapmap]
rs10861336	0.85[CEU][hapmap]
rs1109432	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112347	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs11112350	0.85[CEU][hapmap]
rs11112351	0.85[CEU][hapmap]
rs11112414	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs11112436	0.86[ASN][1000 genomes]
rs11612252	0.85[CEU][hapmap]
rs11613261	0.85[CEU][hapmap]
rs1196750	0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196758	0.96[CEU][hapmap]
rs1196766	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196767	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196776	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196778	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196785	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs1196804	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1196809	0.89[EUR][1000 genomes]
rs1196812	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs1196814	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1196816	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs1196822	0.88[EUR][1000 genomes]
rs1196835	0.88[EUR][1000 genomes]
rs1196836	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs1196838	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1196840	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs1196854	0.90[EUR][1000 genomes]
rs1196856	0.91[EUR][1000 genomes]
rs1196860	0.88[EUR][1000 genomes]
rs1196865	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap]
rs1196866	0.91[EUR][1000 genomes]
rs1196867	0.88[EUR][1000 genomes]
rs1196868	0.91[EUR][1000 genomes]
rs1196878	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1196882	0.89[CEU][hapmap]
rs1201657	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]
rs1201658	0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs12581638	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs1317941	0.87[ASN][1000 genomes]
rs17036869	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs1732378	0.89[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs1732379	0.91[EUR][1000 genomes]
rs1732384	0.80[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2246510	0.96[CEU][hapmap]
rs2264066	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs2374448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440708	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440713	0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs2440717	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs2440719	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs4144468	0.85[CEU][hapmap]
rs4964127	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4964346	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6539196	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs727888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308195	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs7309320	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969800	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7978648	0.85[GIH][hapmap]
rs9143	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]

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	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
4	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1196781	APPL2	cis	cerebellum	SCAN
rs1196781	LOC387882	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:105611200-105628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:105616600-105629000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:105617000-105629000	Weak transcription	Esophagus	oesophagus
6	chr12:105617400-105629000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:105619400-105627400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:105621600-105627200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:105621800-105628600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:105621800-105628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:105622000-105627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:105622000-105629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:105622400-105628400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:105622600-105627800	Weak transcription	HMEC	breast
15	chr12:105622800-105628400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:105623000-105627600	Weak transcription	Thymus	Thymus
17	chr12:105623000-105627600	Weak transcription	Hela-S3	cervix
18	chr12:105623000-105628600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:105623200-105627800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:105623200-105627800	Weak transcription	Fetal Thymus	thymus
21	chr12:105623200-105628000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:105623400-105628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:105623600-105628800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:105624000-105627400	Enhancers	Colon Smooth Muscle	Colon
25	chr12:105624000-105627400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr12:105624200-105627400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:105625000-105628800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:105625000-105628800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:105625200-105628000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:105625200-105628000	Enhancers	Right Ventricle	heart
31	chr12:105625400-105627200	Enhancers	Colonic Mucosa	Colon
32	chr12:105625400-105627200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:105625400-105627200	Weak transcription	A549	lung
34	chr12:105625400-105627600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:105625400-105627800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr12:105625400-105628200	Enhancers	Fetal Heart	heart
37	chr12:105625600-105628000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:105625600-105628000	Active TSS	Right Atrium	heart
39	chr12:105625600-105628000	Weak transcription	NHEK	skin
40	chr12:105625600-105628600	Weak transcription	Placenta	Placenta
41	chr12:105625600-105629000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:105625600-105629000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:105625800-105627200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:105625800-105628600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr12:105625800-105628600	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr12:105626000-105628000	Enhancers	Fetal Intestine Large	intestine
47	chr12:105626000-105628000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr12:105626000-105628200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:105626200-105627800	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:105626200-105627800	Weak transcription	Placenta Amnion	Placenta Amnion

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