Variant report

Variant	rs5914897
Chromosome Location	chrX:57129621-57129622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:57128597..57131476-chrX:57146514..57148118,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226310	Chromatin interaction
ENSG00000186787	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10521485	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12687268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs150099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs204166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2071722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap]
rs2213510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2499549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2499550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2499551	0.81[YRI][hapmap]
rs2499555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap]
rs2516019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2516020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2516023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap]
rs2516025	0.81[YRI][hapmap]
rs378487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs4030473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs538910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs5914036	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs5914037	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5914052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs5914074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs5914874	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs5914963	0.81[YRI][hapmap]
rs5960235	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs5960951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs6611612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6612746	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs6612757	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs697664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs707346	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs912956	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs957721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5914897	SPIN-2	cis	multi-tissue	Pritchard

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:57105800-57134600	Weak transcription	HSMMtube	muscle
2	chrX:57107800-57147200	Weak transcription	Right Ventricle	heart
3	chrX:57108400-57147200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chrX:57109400-57147200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chrX:57114400-57139800	Weak transcription	Colon Smooth Muscle	Colon
6	chrX:57116200-57147200	Weak transcription	HSMM	muscle
7	chrX:57116800-57130600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chrX:57117000-57147800	Weak transcription	Primary B cells from cord blood	blood
9	chrX:57117400-57133400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chrX:57117600-57133000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chrX:57117600-57139000	Weak transcription	GM12878-XiMat	blood
12	chrX:57117600-57147200	Weak transcription	Spleen	Spleen
13	chrX:57118600-57147200	Weak transcription	Thymus	Thymus
14	chrX:57119200-57135400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chrX:57119600-57133200	Weak transcription	Pancreas	Pancrea
16	chrX:57119600-57147200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chrX:57119600-57147200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chrX:57119800-57147400	Weak transcription	Aorta	Aorta
19	chrX:57120000-57135200	Weak transcription	A549	lung
20	chrX:57120000-57147200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chrX:57121600-57147200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chrX:57121800-57130800	Weak transcription	Duodenum Mucosa	Duodenum
23	chrX:57121800-57133200	Weak transcription	Ovary	ovary
24	chrX:57121800-57133400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chrX:57121800-57135200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chrX:57121800-57140000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chrX:57121800-57144200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chrX:57121800-57147200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chrX:57121800-57147200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chrX:57122000-57133400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chrX:57122000-57133400	Weak transcription	Fetal Stomach	stomach
32	chrX:57122000-57135400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chrX:57122000-57138200	Weak transcription	Brain Anterior Caudate	brain
34	chrX:57122000-57147200	Weak transcription	Fetal Intestine Small	intestine
35	chrX:57122000-57147200	Weak transcription	Left Ventricle	heart
36	chrX:57122000-57147200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chrX:57122000-57147400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chrX:57122000-57147400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chrX:57122000-57147400	Weak transcription	Small Intestine	intestine
40	chrX:57122200-57134400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chrX:57122200-57147400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chrX:57122400-57129800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chrX:57122400-57134600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chrX:57122400-57144600	Weak transcription	Fetal Intestine Large	intestine
45	chrX:57122600-57147200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chrX:57126000-57147200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chrX:57127200-57145800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chrX:57128000-57147400	Weak transcription	Primary B cells from peripheral blood	blood
49	chrX:57128400-57135200	Weak transcription	Liver	Liver
50	chrX:57129400-57140600	Weak transcription	Primary T cells from cord blood	blood

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