Variant report

Variant	rs2000875
Chromosome Location	chr11:58981586-58981587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58937186..58939247-chr11:58980596..58982199,2	K562	blood:

Variant related genes	Relation type
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1048444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10792228	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896953	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10896956	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10896958	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11229896	0.87[EUR][1000 genomes]
rs11229898	0.85[EUR][1000 genomes]
rs11229899	0.85[EUR][1000 genomes]
rs12280107	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17153461	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1938593	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1938594	0.86[CHB][hapmap]
rs1945592	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1945593	0.87[EUR][1000 genomes]
rs2211912	0.85[MKK][hapmap];0.86[YRI][hapmap]
rs3847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4938915	0.88[EUR][1000 genomes]
rs4939260	0.96[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4939263	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4939267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4939269	0.80[MEX][hapmap]
rs5023474	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5023475	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61689139	0.87[EUR][1000 genomes]
rs6591510	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6591515	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6591517	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7109866	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7111287	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7113607	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7115130	0.82[GIH][hapmap]
rs7121247	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7129035	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7129362	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7931234	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7938115	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3351601	chr11:58979308-59052763	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2000875	CYBASC3	cis	parietal	SCAN
rs2000875	MPEG1	Cis_1M	lymphoblastoid	RTeQTL
rs2000875	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs2000875	SNORD28	cis	cerebellum	SCAN
rs2000875	CYBASC3	cis	cerebellum	SCAN
rs2000875	MPEG1	cis	lymphoblastoid	seeQTL
rs2000875	MPEG1	cis	Lymphoblastoid	GTEx
rs2000875	UBE2L6	cis	parietal	SCAN
rs2000875	TMX2	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58973400-58983200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:58973600-58982000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:58973800-58984000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:58975400-58986600	Weak transcription	Gastric	stomach
5	chr11:58975800-58981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:58976000-58989400	Weak transcription	Stomach Mucosa	stomach
7	chr11:58977600-58981600	Flanking Active TSS	GM12878-XiMat	blood
8	chr11:58977600-58984000	Weak transcription	Fetal Lung	lung
9	chr11:58978600-58984000	Weak transcription	Colon Smooth Muscle	Colon
10	chr11:58979200-58989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:58979400-58983800	Weak transcription	Fetal Stomach	stomach
12	chr11:58979800-58985200	Weak transcription	Pancreas	Pancrea
13	chr11:58980000-58984200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr11:58980400-58982000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr11:58980400-58984200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:58980400-58984200	Weak transcription	Fetal Thymus	thymus
17	chr11:58980400-58984400	Weak transcription	Fetal Intestine Small	intestine
18	chr11:58980400-58991200	Weak transcription	Fetal Muscle Leg	muscle
19	chr11:58980600-58982600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr11:58980800-58983200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:58981000-58982800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:58981000-58983000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:58981000-58983000	Weak transcription	Placenta	Placenta
24	chr11:58981000-58984000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr11:58981000-58984000	Enhancers	Primary B cells from cord blood	blood
26	chr11:58981000-58984200	Enhancers	Primary B cells from peripheral blood	blood
27	chr11:58981000-58984200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:58981000-58991600	Weak transcription	Spleen	Spleen
29	chr11:58981200-58983600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:58981200-58984000	Weak transcription	Adipose Nuclei	Adipose

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