Variant report

Variant	rs5762816
Chromosome Location	chr22:29206209-29206210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29168673..29170416-chr22:29204780..29206818,2	MCF-7	breast:
2	chr22:28994581..28996472-chr22:29204269..29206724,2	MCF-7	breast:
3	chr22:29203783..29206690-chr22:29212432..29214598,2	K562	blood:
4	chr22:29205328..29207798-chr6:30697845..30700458,2	MCF-7	breast:
5	chr22:29133437..29141650-chr22:29203240..29216422,34	MCF-7	breast:
6	chr22:29126583..29142031-chr22:29203252..29220632,67	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183765	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000159873	Chromatin interaction
ENSG00000226471	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13053879	0.87[EUR][1000 genomes]
rs13056243	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs13056546	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13058031	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs16986825	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs16986838	0.94[CEU][hapmap]
rs16986861	0.94[CEU][hapmap]
rs16986864	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs16987024	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987027	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235431	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2236141	0.86[EUR][1000 genomes]
rs2267131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2347448	0.81[EUR][1000 genomes]
rs28458474	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881634	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34206997	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34298044	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34573837	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34718288	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34751572	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35017742	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35050306	0.81[EUR][1000 genomes]
rs35814864	0.81[EUR][1000 genomes]
rs35829597	0.84[EUR][1000 genomes]
rs35905502	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36112964	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4055	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs5752790	0.86[EUR][1000 genomes]
rs5752794	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752796	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752797	0.83[CEU][hapmap]
rs5752802	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752806	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752810	0.83[CEU][hapmap]
rs5752811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752815	0.83[CEU][hapmap]
rs5752816	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762767	0.94[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs5762774	0.86[EUR][1000 genomes]
rs5762780	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs5762794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762799	0.83[CEU][hapmap]
rs5762809	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5762812	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762814	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762817	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762818	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762819	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762820	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762821	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762822	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762823	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762839	0.83[CEU][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap]
rs5762848	0.83[CEU][hapmap]
rs5762857	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59203761	0.82[EUR][1000 genomes]
rs59224170	0.82[EUR][1000 genomes]
rs60468718	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66471734	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71327317	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71327329	1.00[AFR][1000 genomes]
rs73170633	0.89[EUR][1000 genomes]
rs73170679	0.81[EUR][1000 genomes]
rs739196	0.94[CEU][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	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
3	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
rs5762816	RGL4	cis	parietal	SCAN
rs5762816	MN1	cis	cerebellum	SCAN
rs5762816	SUSD2	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197200-29208200	Weak transcription	Esophagus	oesophagus
2	chr22:29197200-29209800	Weak transcription	Left Ventricle	heart
3	chr22:29197200-29214200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr22:29197400-29214400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr22:29197400-29220400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr22:29197600-29209800	Weak transcription	Ovary	ovary
8	chr22:29197800-29214200	Weak transcription	Right Ventricle	heart
9	chr22:29198000-29225200	Weak transcription	HSMM	muscle
10	chr22:29198200-29218600	Weak transcription	Brain Angular Gyrus	brain
11	chr22:29198400-29208200	Weak transcription	Fetal Lung	lung
12	chr22:29198400-29208400	Weak transcription	Lung	lung
13	chr22:29198400-29209800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr22:29198400-29214000	Weak transcription	Colonic Mucosa	Colon
15	chr22:29198400-29214400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:29198400-29215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr22:29198400-29225200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr22:29198600-29206800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr22:29198600-29207200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr22:29198600-29207200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr22:29198600-29210600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr22:29198600-29211200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr22:29198600-29212600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr22:29198600-29214200	Weak transcription	Colon Smooth Muscle	Colon
25	chr22:29198600-29214400	Weak transcription	Aorta	Aorta
26	chr22:29198600-29214600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr22:29198600-29219400	Weak transcription	NHLF	lung
28	chr22:29198600-29225200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr22:29198600-29225200	Weak transcription	Osteobl	bone
30	chr22:29198600-29231400	Weak transcription	HSMMtube	muscle
31	chr22:29198800-29206800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:29198800-29207200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr22:29198800-29207800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr22:29198800-29214200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr22:29198800-29214400	Weak transcription	Fetal Heart	heart
36	chr22:29198800-29230800	Weak transcription	NHEK	skin
37	chr22:29199000-29208400	Weak transcription	NHDF-Ad	bronchial
38	chr22:29199400-29207400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr22:29200600-29231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr22:29200800-29208200	Weak transcription	Fetal Stomach	stomach
41	chr22:29201000-29206600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr22:29202400-29206600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr22:29203200-29206600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr22:29203800-29206800	Enhancers	Primary hematopoietic stem cells	blood
45	chr22:29203800-29206800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr22:29203800-29208200	Enhancers	Liver	Liver
47	chr22:29204000-29206400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr22:29204000-29206600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr22:29204000-29206800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr22:29204000-29207400	Enhancers	Small Intestine	intestine

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