Variant report

Variant	rs4765905
Chromosome Location	chr12:2349584-2349585
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:2348220..2352908-chr12:2354792..2357849,4	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024582	0.92[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs10744560	0.96[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10774034	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10774035	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774036	0.96[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10848642	1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11062159	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11062161	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs11062162	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs11062166	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11062170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108073	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs1108074	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1108075	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1108221	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1108222	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12311439	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12315711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424245	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2007044	0.81[CEU][hapmap]
rs2159100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190771	0.86[ASN][1000 genomes]
rs2239038	0.82[MEX][hapmap]
rs2370414	0.82[MEX][hapmap]
rs3922316	0.86[ASN][1000 genomes]
rs4298967	0.92[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs4765904	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7297582	0.82[JPT][hapmap];0.82[TSI][hapmap]
rs758170	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs769087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965923	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Schizophrenia	21926974	GWAS catalog
Schizophrenia	22688191	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4765905	SLC6A12	cis	parietal	SCAN
rs4765905	CACNA1C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2339000-2350600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:2339600-2349800	Weak transcription	Spleen	Spleen
3	chr12:2343000-2352600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:2344400-2349600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:2344400-2365000	Weak transcription	Aorta	Aorta
6	chr12:2345800-2351400	Enhancers	Right Atrium	heart
7	chr12:2346600-2351200	Enhancers	Stomach Smooth Muscle	stomach
8	chr12:2347400-2352000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:2347600-2350400	Enhancers	Fetal Muscle Leg	muscle
10	chr12:2347800-2358200	Enhancers	Right Ventricle	heart
11	chr12:2348000-2351200	Weak transcription	Fetal Thymus	thymus
12	chr12:2348200-2349800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr12:2348200-2350200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr12:2348200-2350200	Bivalent Enhancer	Fetal Stomach	stomach
15	chr12:2348400-2349600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:2348600-2351600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:2348600-2352200	Weak transcription	NHLF	lung
18	chr12:2348800-2349600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:2348800-2350000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:2349000-2349600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr12:2349000-2349600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:2349000-2349600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:2349000-2349800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr12:2349000-2350600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:2349000-2351800	Enhancers	Left Ventricle	heart
26	chr12:2349000-2352400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:2349000-2353200	Weak transcription	Brain Germinal Matrix	brain
28	chr12:2349000-2353600	Weak transcription	Ovary	ovary
29	chr12:2349200-2349600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:2349200-2349600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:2349200-2349800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:2349200-2349800	Enhancers	Brain Angular Gyrus	brain
33	chr12:2349200-2350000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr12:2349200-2351000	Enhancers	Colon Smooth Muscle	Colon
35	chr12:2349200-2351400	Enhancers	Rectal Smooth Muscle	rectum
36	chr12:2349200-2352000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:2349400-2349600	Flanking Active TSS	Fetal Heart	heart
38	chr12:2349400-2349600	Weak transcription	Lung	lung
39	chr12:2349400-2350200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
40	chr12:2349400-2351200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:2349400-2364800	Weak transcription	Fetal Brain Male	brain

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