Variant report

Variant	rs542998
Chromosome Location	chr11:63487386-63487387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63475402..63478468-chr11:63484707..63487659,3	K562	blood:
2	chr11:63437687..63440322-chr11:63486788..63490185,4	K562	blood:
3	chr11:63485183..63488338-chr11:63489769..63491741,3	K562	blood:
4	chr11:63485885..63488439-chr11:63488604..63490732,2	MCF-7	breast:
5	chr11:63486022..63488708-chr11:63493925..63495605,2	K562	blood:

Variant related genes	Relation type
ENSG00000184743	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10897442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231545	0.82[YRI][hapmap]
rs1186605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186941	0.85[MEX][hapmap]
rs1404500	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17615385	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1789218	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2509744	0.85[MEX][hapmap]
rs2850617	0.83[AFR][1000 genomes]
rs2959872	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959880	0.85[MEX][hapmap]
rs3016865	0.85[MEX][hapmap]
rs3758647	1.00[CHB][hapmap]
rs41509648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs474548	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500991	0.85[MEX][hapmap]
rs517700	0.85[MEX][hapmap]
rs520908	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs522648	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523093	0.85[MEX][hapmap]
rs542966	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545539	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567756	0.85[MEX][hapmap]
rs580083	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580695	0.85[MEX][hapmap]
rs61928249	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928251	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111395	0.85[MEX][hapmap]
rs7113325	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121664	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122132	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7128970	0.85[MEX][hapmap]
rs7943981	0.85[MEX][hapmap]
rs7945972	0.85[MEX][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	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv832183	chr11:63416678-63564565	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv897628	chr11:63456478-63508334	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs542998	RASGRP2	cis	parietal	SCAN
rs542998	PLA2G16	cis	cerebellum	SCAN
rs542998	GNG3	cis	cerebellum	SCAN
rs542998	SAC3D1	cis	cerebellum	SCAN
rs542998	SLC22A9	cis	cerebellum	SCAN
rs542998	FLRT1	cis	cerebellum	SCAN
rs542998	NAA40	cis	cerebellum	SCAN
rs542998	MTA2	cis	cerebellum	SCAN
rs542998	SNORD25	cis	parietal	SCAN
rs542998	ANKRD13D	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63450800-63517400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr11:63456800-63490000	Weak transcription	Primary B cells from cord blood	blood
3	chr11:63459600-63516600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:63463200-63516200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:63464200-63489600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:63466200-63490000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:63467400-63497200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:63467600-63488200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:63467600-63489200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:63467600-63489800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:63467600-63516000	Weak transcription	Thymus	Thymus
12	chr11:63467600-63517600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:63469400-63497600	Weak transcription	Left Ventricle	heart
14	chr11:63473000-63488800	Weak transcription	Esophagus	oesophagus
15	chr11:63473000-63516000	Weak transcription	Lung	lung
16	chr11:63473000-63518000	Weak transcription	Aorta	Aorta
17	chr11:63473000-63529400	Weak transcription	Right Ventricle	heart
18	chr11:63473200-63487800	Weak transcription	Brain Germinal Matrix	brain
19	chr11:63474800-63501200	Weak transcription	Fetal Stomach	stomach
20	chr11:63477000-63487600	Weak transcription	NH-A	brain
21	chr11:63477400-63498000	Weak transcription	NHLF	lung
22	chr11:63478400-63488600	Weak transcription	HSMMtube	muscle
23	chr11:63478400-63492400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:63478400-63493600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:63478400-63496000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:63478400-63496400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:63478600-63490200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:63478800-63488400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:63478800-63495200	Weak transcription	Fetal Intestine Large	intestine
30	chr11:63478800-63517200	Weak transcription	Fetal Intestine Small	intestine
31	chr11:63479600-63488600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:63479600-63493000	Weak transcription	Placenta	Placenta
33	chr11:63480600-63509000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr11:63481000-63501000	Weak transcription	Fetal Brain Female	brain
35	chr11:63481000-63517600	Weak transcription	Spleen	Spleen
36	chr11:63481600-63505800	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:63481800-63512800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:63482400-63505000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:63483400-63489600	Weak transcription	HMEC	breast
40	chr11:63483400-63517000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:63483600-63494000	Weak transcription	HepG2	liver
42	chr11:63483800-63488200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr11:63484000-63488600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:63484000-63504600	Weak transcription	A549	lung
45	chr11:63484400-63490200	Weak transcription	Fetal Brain Male	brain
46	chr11:63484600-63494000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:63485000-63491200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr11:63485600-63488600	Strong transcription	HSMM	muscle
49	chr11:63485800-63487400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:63486000-63487400	Strong transcription	GM12878-XiMat	blood

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