Variant report

Variant	rs5914428
Chromosome Location	chrX:55746426-55746427
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:55743068..55746123-chrX:55746140..55748206,3	MCF-7	breast:
2	chrX:55744400..55746852-chrX:55753223..55755177,2	MCF-7	breast:
3	chrX:55746055..55747904-chrX:55749271..55751160,2	MCF-7	breast:

Variant related genes	Relation type
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];0.81[TSI][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];0.81[TSI][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]
rs5913857	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]
rs5913859	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];0.81[TSI][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];0.97[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];0.81[TSI][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
rs5914428	RRAGB	cis	lymphoblastoid	seeQTL
rs5914428	SPIN-2	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:55743600-55747600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chrX:55744800-55747600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chrX:55744800-55763200	Weak transcription	Aorta	Aorta
4	chrX:55744800-55763600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chrX:55744800-55774600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chrX:55745000-55746800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chrX:55745000-55763400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chrX:55745200-55746800	Enhancers	Primary T cells from cord blood	blood
9	chrX:55745200-55746800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chrX:55745200-55747000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chrX:55745200-55747000	Weak transcription	Fetal Muscle Trunk	muscle
12	chrX:55745200-55747400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chrX:55745200-55747400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chrX:55745200-55747400	Weak transcription	Fetal Thymus	thymus
15	chrX:55745200-55747400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chrX:55745200-55747400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chrX:55745200-55749200	Weak transcription	Fetal Stomach	stomach
18	chrX:55745200-55750000	Weak transcription	Ovary	ovary
19	chrX:55745200-55756000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chrX:55745200-55756200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chrX:55745200-55756200	Weak transcription	Lung	lung
22	chrX:55745200-55756200	Weak transcription	NHLF	lung
23	chrX:55745200-55756400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chrX:55745200-55756400	Weak transcription	Brain Germinal Matrix	brain
25	chrX:55745200-55757400	Weak transcription	Fetal Lung	lung
26	chrX:55745200-55757600	Weak transcription	Left Ventricle	heart
27	chrX:55745200-55758000	Weak transcription	Placenta	Placenta
28	chrX:55745200-55758200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chrX:55745200-55758600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chrX:55745200-55763200	Weak transcription	Pancreas	Pancrea
31	chrX:55745200-55763400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chrX:55745200-55763600	Weak transcription	Gastric	stomach
33	chrX:55745200-55763800	Weak transcription	Esophagus	oesophagus
34	chrX:55745200-55765000	Weak transcription	Colonic Mucosa	Colon
35	chrX:55745200-55773400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chrX:55745200-55781200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chrX:55745200-55785800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chrX:55745400-55746600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chrX:55745400-55746600	Enhancers	Dnd41	blood
40	chrX:55745400-55746800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chrX:55745400-55747000	Weak transcription	Fetal Muscle Leg	muscle
42	chrX:55745400-55747200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chrX:55745400-55747400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chrX:55745400-55747600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chrX:55745400-55747600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chrX:55745400-55747600	Weak transcription	Fetal Kidney	kidney
47	chrX:55745400-55749200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chrX:55745400-55749200	Weak transcription	Fetal Intestine Large	intestine
49	chrX:55745400-55754400	Weak transcription	Brain Hippocampus Middle	brain
50	chrX:55745400-55755200	Weak transcription	Stomach Smooth Muscle	stomach

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