Variant report

Variant	rs12712626
Chromosome Location	chr2:39092051-39092052
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39060039..39062647-chr2:39091366..39093415,2	K562	blood:
2	chr2:39089505..39093700-chr2:39094409..39098372,5	K562	blood:
3	chr2:39065831..39067433-chr2:39089862..39092131,2	K562	blood:
4	chr2:39082200..39083996-chr2:39090256..39092735,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1010859	0.81[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap]
rs10779923	0.87[GIH][hapmap];0.91[MEX][hapmap]
rs11124651	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11675110	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11689954	0.81[CHB][hapmap]
rs12373604	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12465365	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12623330	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12712625	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap]
rs12712627	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13029388	0.88[CEU][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1530852	0.81[CEU][hapmap]
rs17494315	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1901289	0.92[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3099937	0.91[AFR][1000 genomes]
rs3099956	0.81[CHB][hapmap]
rs3099958	0.81[CHB][hapmap]
rs3099994	0.81[EUR][1000 genomes]
rs3099995	0.85[EUR][1000 genomes]
rs3100000	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes]
rs3112159	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs3112163	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs373300	0.83[YRI][hapmap]
rs3923144	0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4133043	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4265996	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4641916	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4670266	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4670899	0.83[GIH][hapmap]
rs6710418	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6732083	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6734584	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6738069	0.81[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap]
rs6738403	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6741088	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6744514	0.82[YRI][hapmap]
rs7419838	0.83[TSI][hapmap]
rs7565111	0.81[CHB][hapmap]
rs7586929	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7598922	0.92[CEU][hapmap];0.92[GIH][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9808136	0.85[YRI][hapmap]

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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12712626	DHX57	cis	multi-tissue	Pritchard
rs12712626	MORN2	cis	parietal	SCAN
rs12712626	ITGB1	trans	parietal	SCAN
rs12712626	MFN1	trans	parietal	SCAN
rs12712626	DHX57	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:39038800-39102200	Weak transcription	Gastric	stomach
3	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
5	chr2:39072200-39095400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:39080000-39102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:39081200-39102200	Weak transcription	Right Ventricle	heart
8	chr2:39081200-39102200	Weak transcription	Spleen	Spleen
9	chr2:39081200-39102400	Weak transcription	Pancreas	Pancrea
10	chr2:39081600-39093400	Weak transcription	Aorta	Aorta
11	chr2:39086000-39094400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:39086400-39101800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:39087600-39095400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:39088200-39102000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:39089200-39101800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:39089200-39101800	Weak transcription	Fetal Heart	heart
17	chr2:39089400-39093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:39089400-39093200	Weak transcription	NHEK	skin
19	chr2:39089400-39094000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:39089400-39094200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:39089400-39094600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:39089400-39095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:39089400-39101200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:39089400-39102000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:39089400-39102200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:39089400-39102200	Weak transcription	Ovary	ovary
27	chr2:39089400-39102200	Weak transcription	Small Intestine	intestine
28	chr2:39089600-39092400	Weak transcription	Psoas Muscle	Psoas
29	chr2:39089600-39093200	Weak transcription	NH-A	brain
30	chr2:39089600-39093400	Weak transcription	Fetal Brain Male	brain
31	chr2:39089600-39093800	Weak transcription	Fetal Stomach	stomach
32	chr2:39089600-39094000	Weak transcription	Thymus	Thymus
33	chr2:39089600-39094000	Weak transcription	Hela-S3	cervix
34	chr2:39089600-39094600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:39089600-39101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:39089600-39102000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:39089600-39102000	Weak transcription	NHLF	lung
38	chr2:39089600-39102400	Weak transcription	Lung	lung
39	chr2:39089800-39097200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:39089800-39101800	Weak transcription	Brain Substantia Nigra	brain
41	chr2:39090000-39093400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:39090000-39094200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:39090000-39102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:39090000-39102000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:39090200-39093200	Weak transcription	GM12878-XiMat	blood
46	chr2:39090200-39093400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:39090200-39094600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:39090200-39101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:39090200-39102400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:39090400-39093000	Weak transcription	Placenta	Placenta

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