Variant report

Variant	rs6005915
Chromosome Location	chr22:29233262-29233263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29227240..29229282-chr22:29232209..29234813,2	MCF-7	breast:
2	chr22:29190538..29192302-chr22:29232291..29234137,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12165962	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap]
rs12628211	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs132530	0.87[YRI][hapmap]
rs132531	0.95[JPT][hapmap];0.82[MEX][hapmap]
rs132533	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs132536	0.95[JPT][hapmap]
rs132548	0.95[JPT][hapmap];0.82[MEX][hapmap]
rs1894590	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs2064261	0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs2097461	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2213645	0.89[JPT][hapmap]
rs2239815	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs2269577	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2347447	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs3788409	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs469990	0.95[JPT][hapmap];0.82[MEX][hapmap]
rs469991	0.95[JPT][hapmap]
rs4822998	0.88[JPT][hapmap]
rs5752797	0.85[CEU][hapmap]
rs5752809	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs5752810	0.85[CEU][hapmap]
rs5752812	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs5752815	0.85[CEU][hapmap]
rs5762784	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs5762788	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs5762795	0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs5762799	0.85[CEU][hapmap];0.85[YRI][hapmap]
rs5762803	0.81[AMR][1000 genomes]
rs5762839	0.85[CEU][hapmap]
rs5762848	0.85[CEU][hapmap]
rs5762853	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5762863	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5762864	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5762867	0.82[EUR][1000 genomes]
rs5762874	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs5762881	0.95[JPT][hapmap]
rs5762882	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs5762936	0.90[JPT][hapmap]
rs5997400	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs5997404	0.83[ASW][hapmap];0.84[YRI][hapmap]
rs5997408	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs6005879	0.85[YRI][hapmap]
rs6005881	0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs6005900	0.82[AFR][1000 genomes]
rs6005905	0.88[YRI][hapmap]
rs6005907	0.83[ASW][hapmap];0.82[LWK][hapmap];0.88[YRI][hapmap]
rs6005927	0.83[EUR][1000 genomes]
rs6005929	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6519764	0.88[YRI][hapmap]
rs6519766	0.95[JPT][hapmap];0.91[MEX][hapmap]
rs7284322	0.85[YRI][hapmap]
rs7287124	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7287806	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs7287918	0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs763073	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs9620841	0.95[JPT][hapmap];0.91[MEX][hapmap]
rs9625619	0.95[JPT][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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6005915	XBP1	cis	cerebellum	SCAN
rs6005915	MN1	cis	cerebellum	SCAN
rs6005915	ZNRF3	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29214800-29242200	Weak transcription	Aorta	Aorta
2	chr22:29216000-29233800	Weak transcription	Left Ventricle	heart
3	chr22:29216000-29238600	Weak transcription	Spleen	Spleen
4	chr22:29219400-29234800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr22:29224000-29237400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr22:29225400-29242000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr22:29226000-29248800	Weak transcription	Primary T cells from cord blood	blood
8	chr22:29226200-29234600	Weak transcription	Brain Substantia Nigra	brain
9	chr22:29226200-29234800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr22:29226200-29239600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr22:29226200-29242800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr22:29226600-29241800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr22:29226600-29242200	Weak transcription	Fetal Muscle Leg	muscle
14	chr22:29227800-29235000	Weak transcription	Liver	Liver
15	chr22:29229400-29241800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr22:29230400-29236800	Weak transcription	Fetal Stomach	stomach
17	chr22:29231200-29239200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr22:29232200-29233800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr22:29232200-29234600	Weak transcription	Fetal Intestine Large	intestine
20	chr22:29232200-29235600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr22:29232600-29236000	Weak transcription	Fetal Intestine Small	intestine
22	chr22:29233000-29234200	Enhancers	Dnd41	blood

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