Variant report

Variant	rs13227951
Chromosome Location	chr7:66213108-66213109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66117314..66120062-chr7:66210977..66213938,2	K562	blood:
2	chr7:66203955..66208659-chr7:66209716..66215353,8	K562	blood:
3	chr7:66211368..66213994-chr7:66217034..66219333,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243335	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000272831	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10234018	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs10249404	0.82[CEU][hapmap]
rs10252765	0.82[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs10263935	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs10272546	0.85[EUR][1000 genomes]
rs10274773	0.87[EUR][1000 genomes]
rs10950044	0.82[CEU][hapmap]
rs1110414	0.87[EUR][1000 genomes]
rs11766262	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11768727	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11771318	0.88[EUR][1000 genomes]
rs11772264	0.88[EUR][1000 genomes]
rs11772636	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11773829	0.87[EUR][1000 genomes]
rs1553609	0.88[EUR][1000 genomes]
rs1553610	0.88[EUR][1000 genomes]
rs17566701	0.89[EUR][1000 genomes]
rs1860468	0.85[EUR][1000 genomes]
rs1860470	0.84[EUR][1000 genomes]
rs1961155	0.85[EUR][1000 genomes]
rs2003301	0.87[EUR][1000 genomes]
rs2013222	0.82[CEU][hapmap]
rs2016325	0.83[ASN][1000 genomes]
rs2055682	0.82[EUR][1000 genomes]
rs2191268	0.82[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2244022	0.86[GIH][hapmap]
rs2286683	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs2286684	0.87[EUR][1000 genomes]
rs2420824	0.88[EUR][1000 genomes]
rs2659889	0.87[EUR][1000 genomes]
rs2659899	0.84[EUR][1000 genomes]
rs2659906	0.87[EUR][1000 genomes]
rs2659909	0.88[EUR][1000 genomes]
rs2659912	0.87[EUR][1000 genomes]
rs2659915	0.87[EUR][1000 genomes]
rs2659916	0.86[EUR][1000 genomes]
rs2707822	0.88[EUR][1000 genomes]
rs2707827	0.85[EUR][1000 genomes]
rs2707836	0.87[EUR][1000 genomes]
rs2707841	0.87[EUR][1000 genomes]
rs2707845	0.87[EUR][1000 genomes]
rs2707849	0.87[EUR][1000 genomes]
rs2707850	0.88[EUR][1000 genomes]
rs2707852	0.85[EUR][1000 genomes]
rs2707853	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs2707854	0.82[CEU][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2707856	0.82[CEU][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs3069894	0.85[EUR][1000 genomes]
rs34191148	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34356500	0.84[EUR][1000 genomes]
rs35130766	0.84[EUR][1000 genomes]
rs35526611	0.82[EUR][1000 genomes]
rs35986979	0.83[EUR][1000 genomes]
rs3764903	0.82[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs3778909	0.82[EUR][1000 genomes]
rs3778917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3800812	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs3800820	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs3800823	0.87[EUR][1000 genomes]
rs3857688	0.87[EUR][1000 genomes]
rs4273746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4279493	0.88[EUR][1000 genomes]
rs4717310	0.86[EUR][1000 genomes]
rs4717319	0.86[EUR][1000 genomes]
rs4718403	0.85[EUR][1000 genomes]
rs62466793	0.87[EUR][1000 genomes]
rs62466794	0.88[EUR][1000 genomes]
rs62467857	0.83[EUR][1000 genomes]
rs6460305	0.82[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap]
rs6460308	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs6460309	0.80[EUR][1000 genomes]
rs6943696	0.82[CEU][hapmap]
rs6949912	0.80[EUR][1000 genomes]
rs6952407	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6958520	0.82[CEU][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs6960778	0.81[EUR][1000 genomes]
rs6979488	0.87[EUR][1000 genomes]
rs7779971	0.87[EUR][1000 genomes]
rs7782320	0.85[EUR][1000 genomes]
rs7783924	0.87[EUR][1000 genomes]
rs7785213	0.87[EUR][1000 genomes]
rs7788576	0.87[EUR][1000 genomes]
rs7789184	0.88[EUR][1000 genomes]
rs7789419	0.81[EUR][1000 genomes]
rs7793569	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs7807930	0.83[EUR][1000 genomes]
rs7807944	0.83[EUR][1000 genomes]
rs801205	0.81[CEU][hapmap]
rs9791890	0.83[EUR][1000 genomes]

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	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs13227951	GUSB	cis	multi-tissue	Pritchard
rs13227951	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs13227951	RP4-756H11.3	cis	Thyroid	GTEx
rs13227951	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs13227951	RABGEF1	cis	cerebellum	SCAN
rs13227951	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs13227951	RABGEF1	cis	parietal	SCAN
rs13227951	RP4-756H11.3	cis	Artery Aorta	GTEx
rs13227951	RP4-756H11.3	cis	lung	GTEx
rs13227951	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13227951	GUSB	cis	Liver	GTEx
rs13227951	RP4-756H11.3	cis	Artery Tibial	GTEx
rs13227951	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs13227951	RP4-756H11.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66206400-66216600	Weak transcription	Spleen	Spleen
2	chr7:66206800-66213600	Weak transcription	Small Intestine	intestine
3	chr7:66206800-66216400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:66206800-66223400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:66206800-66232600	Weak transcription	Primary T cells from cord blood	blood
6	chr7:66206800-66238800	Weak transcription	Aorta	Aorta
7	chr7:66207000-66213800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:66207000-66213800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:66207000-66216200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:66207000-66216400	Weak transcription	Right Atrium	heart
11	chr7:66207000-66216600	Weak transcription	Esophagus	oesophagus
12	chr7:66207000-66222200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr7:66207000-66227400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:66207000-66227400	Weak transcription	Fetal Stomach	stomach
15	chr7:66207000-66230600	Weak transcription	Fetal Intestine Large	intestine
16	chr7:66207000-66230600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:66207000-66234000	Weak transcription	Fetal Thymus	thymus
18	chr7:66207000-66238400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:66207000-66238400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:66207000-66255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:66207200-66213400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:66207200-66213600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:66207200-66223400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr7:66207400-66213200	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:66207600-66213600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:66207600-66213800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr7:66207600-66214000	Weak transcription	Gastric	stomach
28	chr7:66207600-66220400	Weak transcription	Brain Angular Gyrus	brain
29	chr7:66207600-66220400	Weak transcription	Brain Substantia Nigra	brain
30	chr7:66207600-66223200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:66207600-66223400	Weak transcription	K562	blood
32	chr7:66207600-66239800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:66207800-66219800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr7:66207800-66220600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:66207800-66225800	Weak transcription	Fetal Muscle Leg	muscle
36	chr7:66208000-66213800	Weak transcription	Placenta	Placenta
37	chr7:66208000-66215800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:66208000-66216400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr7:66208000-66217800	Weak transcription	Right Ventricle	heart
40	chr7:66208000-66219400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr7:66208000-66230600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr7:66208000-66232400	Weak transcription	Thymus	Thymus
43	chr7:66208000-66236800	Weak transcription	Dnd41	blood
44	chr7:66208000-66238000	Weak transcription	A549	lung
45	chr7:66208000-66238600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:66208000-66238600	Weak transcription	Brain Germinal Matrix	brain
47	chr7:66208000-66240800	Weak transcription	HSMMtube	muscle
48	chr7:66208000-66241800	Weak transcription	Hela-S3	cervix
49	chr7:66208200-66213800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr7:66208400-66219400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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