Variant report

Variant	rs5913857
Chromosome Location	chrX:55747951-55747952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chrX:55747827-55748058	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:55743068..55746123-chrX:55746140..55748206,3	MCF-7	breast:

Variant related genes	Relation type
RRAGB	TF binding region
ENSG00000083750	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1007153	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12557467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1325572	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs1325573	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1473760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1473761	1.00[YRI][hapmap]
rs17277280	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1927597	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2375466	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4826281	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826283	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826287	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4826413	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5000659	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5913859	1.00[YRI][hapmap]
rs5914428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5914432	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs5914433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5914434	1.00[YRI][hapmap]
rs5914436	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs5914440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5960093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5960480	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs6611431	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs6612359	1.00[YRI][hapmap]
rs6612417	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs913440	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5913857	SPIN-2	cis	multi-tissue	Pritchard
rs5913857	RRAGB	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:55744800-55763200	Weak transcription	Aorta	Aorta
2	chrX:55744800-55763600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chrX:55744800-55774600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chrX:55745000-55763400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chrX:55745200-55749200	Weak transcription	Fetal Stomach	stomach
6	chrX:55745200-55750000	Weak transcription	Ovary	ovary
7	chrX:55745200-55756000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chrX:55745200-55756200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chrX:55745200-55756200	Weak transcription	Lung	lung
10	chrX:55745200-55756200	Weak transcription	NHLF	lung
11	chrX:55745200-55756400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chrX:55745200-55756400	Weak transcription	Brain Germinal Matrix	brain
13	chrX:55745200-55757400	Weak transcription	Fetal Lung	lung
14	chrX:55745200-55757600	Weak transcription	Left Ventricle	heart
15	chrX:55745200-55758000	Weak transcription	Placenta	Placenta
16	chrX:55745200-55758200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chrX:55745200-55758600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chrX:55745200-55763200	Weak transcription	Pancreas	Pancrea
19	chrX:55745200-55763400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chrX:55745200-55763600	Weak transcription	Gastric	stomach
21	chrX:55745200-55763800	Weak transcription	Esophagus	oesophagus
22	chrX:55745200-55765000	Weak transcription	Colonic Mucosa	Colon
23	chrX:55745200-55773400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chrX:55745200-55781200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chrX:55745200-55785800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chrX:55745400-55749200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chrX:55745400-55749200	Weak transcription	Fetal Intestine Large	intestine
28	chrX:55745400-55754400	Weak transcription	Brain Hippocampus Middle	brain
29	chrX:55745400-55755200	Weak transcription	Stomach Smooth Muscle	stomach
30	chrX:55745400-55756000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chrX:55745400-55756000	Weak transcription	Osteobl	bone
32	chrX:55745400-55756400	Weak transcription	Primary hematopoietic stem cells	blood
33	chrX:55745400-55756800	Weak transcription	HMEC	breast
34	chrX:55745400-55758400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chrX:55745400-55758400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chrX:55745400-55762000	Weak transcription	Brain Substantia Nigra	brain
37	chrX:55745400-55762200	Weak transcription	Brain Cingulate Gyrus	brain
38	chrX:55745400-55763200	Weak transcription	Thymus	Thymus
39	chrX:55745400-55763400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chrX:55745400-55763400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chrX:55745400-55763400	Weak transcription	Right Ventricle	heart
42	chrX:55745400-55764800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chrX:55745400-55765600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chrX:55745400-55766200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chrX:55745400-55769400	Weak transcription	Rectal Smooth Muscle	rectum
46	chrX:55745400-55789800	Weak transcription	NHDF-Ad	bronchial
47	chrX:55745400-55791000	Weak transcription	Psoas Muscle	Psoas
48	chrX:55745400-55791000	Weak transcription	HSMMtube	muscle
49	chrX:55745600-55756000	Weak transcription	Fetal Brain Female	brain
50	chrX:55745600-55770800	Weak transcription	K562	blood

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