Variant report

Variant	rs1798710
Chromosome Location	chr12:57815922-57815923
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57795305..57796807-chr12:57813980..57816529,2	MCF-7	breast:
2	chr12:57814282..57817736-chr12:57822855..57825483,5	MCF-7	breast:
3	chr12:57811921..57813504-chr12:57815181..57816847,2	K562	blood:
4	chr12:57813409..57817246-chr12:57818021..57820762,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179912	Chromatin interaction
ENSG00000258001	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10747777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10747778	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10783818	0.80[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10783819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10783823	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876976	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10876977	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876978	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876980	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876981	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876983	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172156	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs11172165	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172169	0.89[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs11172170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172190	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172191	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11172205	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172211	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172214	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172222	0.80[EUR][1000 genomes]
rs11609986	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs12230111	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12296766	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs12310220	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs12423654	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12579911	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12812140	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1284252	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2063778	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280139	0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs28504983	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3923885	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap]
rs4075325	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs4108243	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760193	0.80[ASN][1000 genomes]
rs4760228	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760244	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760305	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760306	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760308	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs4760348	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4760356	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760357	0.82[ASN][1000 genomes]
rs481196	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs491750	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs492749	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs512223	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs533975	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs537482	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs543410	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs560048	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs568793	0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs575153	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6581134	0.82[ASW][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap]
rs6581135	0.81[ASN][1000 genomes]
rs6581136	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581139	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7132367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133366	0.81[EUR][1000 genomes]
rs7133939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7135142	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs7298418	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7303070	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7307059	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7309659	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7313824	0.80[ASN][1000 genomes]
rs7398058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7486863	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs7977908	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7980310	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9738004	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[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	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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 lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1798710	SPRY2	trans	lymphoblastoid	seeQTL
rs1798710	OR6C4	cis	parietal	SCAN
rs1798710	DKFZP586D0919	cis	multi-tissue	Pritchard
rs1798710	XRCC6BP1	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57753200-57823800	Weak transcription	Esophagus	oesophagus
2	chr12:57766200-57816000	Weak transcription	Fetal Lung	lung
3	chr12:57770800-57824000	Weak transcription	Gastric	stomach
4	chr12:57774400-57819200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:57780800-57823200	Weak transcription	Spleen	Spleen
6	chr12:57783800-57823200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:57784200-57818000	Weak transcription	HSMM	muscle
8	chr12:57784400-57816400	Weak transcription	NHLF	lung
9	chr12:57788600-57823200	Weak transcription	NHDF-Ad	bronchial
10	chr12:57789200-57823000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:57789400-57823200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:57789600-57816200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:57789800-57816000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:57789800-57816000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:57789800-57816200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:57790000-57816200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:57790000-57823200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:57795400-57816000	Weak transcription	Brain Angular Gyrus	brain
19	chr12:57795400-57822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:57795400-57823000	Weak transcription	Brain Substantia Nigra	brain
21	chr12:57795400-57823200	Weak transcription	Adipose Nuclei	Adipose
22	chr12:57795400-57823200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:57795400-57823200	Weak transcription	HMEC	breast
24	chr12:57795400-57823600	Weak transcription	Aorta	Aorta
25	chr12:57795800-57823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:57795800-57823200	Weak transcription	Right Ventricle	heart
27	chr12:57805800-57822600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:57806200-57822200	Weak transcription	Small Intestine	intestine
29	chr12:57808000-57823000	Weak transcription	NH-A	brain
30	chr12:57809200-57816000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:57809400-57823000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:57809400-57823200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:57809600-57816000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:57809600-57822800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:57809600-57823200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:57809600-57823200	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:57809600-57823400	Weak transcription	Fetal Kidney	kidney
38	chr12:57809800-57823200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:57810200-57823400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:57810200-57823400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:57810600-57816000	Weak transcription	Osteobl	bone
42	chr12:57810600-57822400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:57811000-57816200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:57811200-57823000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:57811400-57822800	Weak transcription	A549	lung
46	chr12:57812000-57822800	Weak transcription	Hela-S3	cervix
47	chr12:57812000-57823200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:57812200-57816000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:57812200-57823200	Weak transcription	Brain Anterior Caudate	brain
50	chr12:57812200-57823200	Weak transcription	Brain Inferior Temporal Lobe	brain

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