Variant report

Variant	rs12203040
Chromosome Location	chr6:140167314-140167315
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11155089	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12195861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205724	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1022881	chr6:140098646-140172570	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12203040	NMBR	cis	parietal	SCAN
rs12203040	IL22RA2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140161200-140167800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:140161200-140167800	Weak transcription	Psoas Muscle	Psoas
3	chr6:140161400-140168200	Weak transcription	Adipose Nuclei	Adipose
4	chr6:140161600-140167600	Weak transcription	Liver	Liver
5	chr6:140163200-140167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:140163600-140167400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:140163600-140167400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:140163600-140167400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:140163600-140167600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:140167000-140169000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:140167200-140167400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr6:140167200-140167600	Enhancers	Stomach Smooth Muscle	stomach
13	chr6:140167200-140167800	Enhancers	Fetal Intestine Small	intestine
14	chr6:140167200-140167800	Enhancers	Fetal Kidney	kidney
15	chr6:140167200-140168000	Enhancers	Fetal Intestine Large	intestine
16	chr6:140167200-140168000	Enhancers	Stomach Mucosa	stomach
17	chr6:140167200-140168600	Enhancers	Primary B cells from cord blood	blood
18	chr6:140167200-140168600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr6:140167200-140168600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:140167200-140168600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr6:140167200-140169000	Enhancers	Primary hematopoietic stem cells	blood

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