Variant report

Variant	rs5762839
Chromosome Location	chr22:29231447-29231448
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	chr22:29227984..29230495-chr22:29230586..29232101,2	MCF-7	breast:
2	chr22:29167261..29170081-chr22:29228738..29231963,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10427628	0.86[EUR][1000 genomes]
rs12170231	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs13058031	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs13058460	0.82[ASN][1000 genomes]
rs2267131	0.83[CEU][hapmap]
rs2301428	0.83[CEU][hapmap]
rs5752803	0.82[CEU][hapmap]
rs5752808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752811	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.93[AFR][1000 genomes]
rs5752814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762767	0.87[MKK][hapmap]
rs5762814	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs5762816	0.83[CEU][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap]
rs5762826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762829	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762852	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762855	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762858	0.83[EUR][1000 genomes]
rs5762879	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap]
rs5997409	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997410	0.84[AMR][1000 genomes]
rs6005915	0.85[CEU][hapmap]
rs6005917	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625595	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625600	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5762839	FLJ33814	cis	multi-tissue	Pritchard
rs5762839	SUSD2	cis	parietal	SCAN
rs5762839	RGL4	cis	parietal	SCAN
rs5762839	MN1	cis	cerebellum	SCAN
rs5762839	C22orf36	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:29214800-29242200	Weak transcription	Aorta	Aorta
3	chr22:29215600-29231600	Weak transcription	Right Ventricle	heart
4	chr22:29216000-29231600	Weak transcription	Placenta	Placenta
5	chr22:29216000-29232800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr22:29216000-29233800	Weak transcription	Left Ventricle	heart
7	chr22:29216000-29238600	Weak transcription	Spleen	Spleen
8	chr22:29218200-29231800	Weak transcription	Gastric	stomach
9	chr22:29219400-29234800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr22:29219600-29231800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr22:29224000-29237400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr22:29225400-29242000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr22:29225800-29231600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr22:29225800-29231800	Weak transcription	HSMM	muscle
15	chr22:29225800-29233000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr22:29226000-29231600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr22:29226000-29233000	Weak transcription	Dnd41	blood
18	chr22:29226000-29248800	Weak transcription	Primary T cells from cord blood	blood
19	chr22:29226200-29234600	Weak transcription	Brain Substantia Nigra	brain
20	chr22:29226200-29234800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr22:29226200-29239600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr22:29226200-29242800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr22:29226400-29231600	Weak transcription	Pancreas	Pancrea
24	chr22:29226400-29231600	Weak transcription	Thymus	Thymus
25	chr22:29226600-29231800	Weak transcription	Fetal Intestine Large	intestine
26	chr22:29226600-29241800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr22:29226600-29242200	Weak transcription	Fetal Muscle Leg	muscle
28	chr22:29227800-29235000	Weak transcription	Liver	Liver
29	chr22:29228200-29231800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr22:29228200-29231800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr22:29228400-29231600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr22:29229400-29241800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr22:29230200-29231600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr22:29230400-29231600	Weak transcription	Lung	lung
35	chr22:29230400-29236800	Weak transcription	Fetal Stomach	stomach
36	chr22:29230600-29231600	Weak transcription	Fetal Intestine Small	intestine
37	chr22:29231200-29239200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr22:29231400-29231800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr22:29231400-29232200	Enhancers	HSMMtube	muscle

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