Variant report

Variant	rs12746592
Chromosome Location	chr1:155505967-155505968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155502169..155504440-chr1:155504548..155506346,2	K562	blood:
2	chr1:155476586..155479575-chr1:155503974..155506052,2	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10752611	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796943	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10796944	0.86[AMR][1000 genomes]
rs10796945	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796946	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796947	0.95[ASN][1000 genomes]
rs10908465	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10908466	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908467	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908469	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908470	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908472	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908479	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs11264363	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11264367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264369	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264370	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11264371	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11264372	0.89[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11264374	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264383	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264386	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264393	0.85[EUR][1000 genomes]
rs11264397	0.83[EUR][1000 genomes]
rs11264398	0.83[EUR][1000 genomes]
rs11582072	0.95[ASN][1000 genomes]
rs12022088	0.83[EUR][1000 genomes]
rs12025532	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12026638	0.89[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12028416	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12030596	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035524	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap]
rs12037824	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12039893	0.83[EUR][1000 genomes]
rs12040100	0.83[EUR][1000 genomes]
rs12041534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12046473	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12047756	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs12067371	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12079134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12081067	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12091730	0.82[AMR][1000 genomes]
rs12093350	0.82[AMR][1000 genomes]
rs12143948	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12239100	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12239114	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs12724079	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12740629	0.81[EUR][1000 genomes]
rs12744132	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs1325908	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1360554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs1556488	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1886905	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs2025669	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2048431	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs2175391	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs2666826	0.90[JPT][hapmap]
rs34124416	0.85[EUR][1000 genomes]
rs34620961	0.81[EUR][1000 genomes]
rs348186	0.80[EUR][1000 genomes]
rs348196	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs35615695	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs3738590	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs3851912	0.85[EUR][1000 genomes]
rs3892792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs475550	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs4971095	0.83[EUR][1000 genomes]
rs5005770	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs56675301	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6427278	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6672128	0.82[EUR][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs6688636	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs6696888	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs670876	0.80[CEU][hapmap]
rs678157	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs71517782	0.82[AMR][1000 genomes]
rs7411786	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7416976	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7521594	0.82[EUR][1000 genomes]
rs7556102	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs821551	0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]

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	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv1800974	chr1:155367680-155510824	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv872468	chr1:155413304-155549562	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12746592	SPRR2D	cis	parietal	SCAN
rs12746592	GBAP1	cis	Artery Tibial	GTEx
rs12746592	YY1AP1	cis	cerebellum	SCAN
rs12746592	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12746592	GBA	cis	Esophagus Mucosa	GTEx
rs12746592	SPRR2A	cis	cerebellum	SCAN
rs12746592	YY1AP1	cis	parietal	SCAN
rs12746592	FDPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155476400-155518200	Weak transcription	HMEC	breast
2	chr1:155477600-155509400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:155478200-155506000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:155478400-155510400	Weak transcription	Stomach Mucosa	stomach
5	chr1:155478400-155518200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:155483200-155524400	Weak transcription	Fetal Brain Female	brain
7	chr1:155483400-155528600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:155485200-155506200	Weak transcription	Thymus	Thymus
9	chr1:155488000-155513400	Weak transcription	Fetal Stomach	stomach
10	chr1:155489000-155506000	Weak transcription	A549	lung
11	chr1:155489800-155506000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:155489800-155516200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:155489800-155529400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:155490000-155513000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:155490400-155506200	Weak transcription	Fetal Intestine Large	intestine
16	chr1:155491000-155509400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:155491200-155506200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:155491200-155521800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:155491400-155523400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:155491600-155516200	Weak transcription	NHEK	skin
21	chr1:155493400-155514200	Weak transcription	Gastric	stomach
22	chr1:155493600-155506000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:155493600-155506200	Weak transcription	Small Intestine	intestine
24	chr1:155496600-155509000	Weak transcription	Dnd41	blood
25	chr1:155496600-155518400	Weak transcription	HSMM	muscle
26	chr1:155496600-155529800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:155497800-155507800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:155497800-155513600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:155498000-155513000	Weak transcription	Hela-S3	cervix
30	chr1:155499600-155517000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:155500000-155516400	Weak transcription	NHDF-Ad	bronchial
32	chr1:155500000-155524400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:155500200-155519800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:155500800-155506000	Weak transcription	Ovary	ovary
35	chr1:155501000-155511800	Weak transcription	Aorta	Aorta
36	chr1:155501800-155511200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:155501800-155523200	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:155502000-155506000	Weak transcription	Fetal Lung	lung
39	chr1:155502000-155506200	Weak transcription	Brain Substantia Nigra	brain
40	chr1:155502000-155508400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:155502000-155509800	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:155502000-155509800	Weak transcription	Fetal Kidney	kidney
43	chr1:155502000-155516200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:155502000-155518000	Weak transcription	Brain Anterior Caudate	brain
45	chr1:155502000-155518800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:155503000-155506000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:155503000-155512000	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr1:155503200-155507200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:155503400-155507200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr1:155503400-155519600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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