Variant report

Variant	rs11628126
Chromosome Location	chr14:69565193-69565194
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69558940..69562138-chr14:69562200..69566674,5	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1007407	1.00[JPT][hapmap]
rs10083451	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10130013	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10131077	0.87[ASN][1000 genomes]
rs10132533	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10134578	0.90[ASN][1000 genomes]
rs10135643	0.89[ASN][1000 genomes]
rs10135971	0.87[ASN][1000 genomes]
rs1013762	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10139873	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10141040	0.87[ASN][1000 genomes]
rs10143302	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10145565	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10146339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10147369	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10148614	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10149232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10498527	0.87[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1105625	0.87[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11158780	0.81[ASN][1000 genomes]
rs11158782	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11158784	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11158785	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11158786	0.86[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11158787	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11158789	0.85[EUR][1000 genomes]
rs11158790	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11158795	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11158798	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1147481	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11622889	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12431846	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12434775	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12435594	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12437418	0.84[ASN][1000 genomes]
rs12589028	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1275407	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1275414	0.85[EUR][1000 genomes]
rs1275415	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1275417	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12879406	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12886715	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12889849	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1626122	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17106754	0.83[CHD][hapmap]
rs1710989	0.87[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs1710990	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1892297	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1914004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2001355	0.87[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2001998	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2012764	1.00[JPT][hapmap]
rs2056153	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2300875	1.00[JPT][hapmap]
rs2331919	0.88[ASN][1000 genomes]
rs28613298	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3173	0.83[CEU][hapmap]
rs3211166	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs4143922	0.83[CHD][hapmap]
rs4338726	0.81[ASN][1000 genomes]
rs4902695	0.95[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs6573869	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs67313346	0.97[EUR][1000 genomes]
rs7148045	1.00[JPT][hapmap]
rs7150225	0.89[EUR][1000 genomes]
rs7160629	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs8008184	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8008735	0.83[CHD][hapmap]
rs8017103	0.81[ASN][1000 genomes]
rs9323521	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9323522	0.91[ASN][1000 genomes]
rs9323524	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11628126	SYNJ2BP	cis	cerebellum	SCAN
rs11628126	RAD51L1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69535600-69565200	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr14:69542600-69570600	Strong transcription	Primary T cells from cord blood	blood
3	chr14:69546200-69583000	Weak transcription	Psoas Muscle	Psoas
4	chr14:69548200-69567400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr14:69550000-69568000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr14:69558600-69569600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr14:69558600-69570400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr14:69558600-69572000	Weak transcription	Brain Germinal Matrix	brain
9	chr14:69558600-69578600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr14:69558800-69565200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:69558800-69567800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr14:69558800-69569400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr14:69558800-69569600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr14:69558800-69570000	Weak transcription	Fetal Brain Female	brain
15	chr14:69558800-69572000	Weak transcription	Esophagus	oesophagus
16	chr14:69558800-69572000	Weak transcription	Spleen	Spleen
17	chr14:69558800-69581600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr14:69558800-69582000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr14:69558800-69595800	Weak transcription	Hela-S3	cervix
20	chr14:69559000-69566200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr14:69559000-69569600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr14:69559000-69583800	Weak transcription	Colonic Mucosa	Colon
23	chr14:69559200-69567800	Weak transcription	Liver	Liver
24	chr14:69559200-69569400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr14:69560000-69565200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr14:69560400-69589400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr14:69560600-69565200	Strong transcription	Primary B cells from cord blood	blood
28	chr14:69560600-69575000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr14:69561000-69565200	Strong transcription	Fetal Intestine Large	intestine
30	chr14:69561200-69567800	Weak transcription	Fetal Intestine Small	intestine
31	chr14:69561200-69568400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr14:69561200-69569600	Weak transcription	GM12878-XiMat	blood
33	chr14:69561200-69572000	Weak transcription	Gastric	stomach
34	chr14:69561200-69577200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr14:69561200-69581600	Weak transcription	Aorta	Aorta
36	chr14:69561200-69581600	Weak transcription	Lung	lung
37	chr14:69561200-69581600	Weak transcription	Pancreas	Pancrea
38	chr14:69561200-69581600	Weak transcription	Small Intestine	intestine
39	chr14:69561400-69567800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr14:69561400-69567800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr14:69561400-69567800	Weak transcription	NHEK	skin
42	chr14:69561400-69569400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr14:69561400-69581600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:69561600-69567800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr14:69561600-69567800	Weak transcription	Adipose Nuclei	Adipose
46	chr14:69561600-69567800	Weak transcription	NHDF-Ad	bronchial
47	chr14:69561600-69569600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr14:69561600-69572000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr14:69561600-69581600	Weak transcription	Brain Angular Gyrus	brain
50	chr14:69561600-69581600	Weak transcription	Brain Inferior Temporal Lobe	brain

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