Variant report

Variant	rs6742593
Chromosome Location	chr2:46890538-46890539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46883898..46887037-chr2:46888701..46892071,3	K562	blood:
2	chr2:46890137..46890667-chr2:47003575..47004531,2	MCF-7	breast:
3	chr2:46880745..46883271-chr2:46889135..46890937,2	MCF-7	breast:
4	chr2:46886567..46889268-chr2:46889432..46892855,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10495935	0.82[CHD][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs17035465	0.87[ASN][1000 genomes]
rs17035488	0.82[CHD][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs17035489	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs17035491	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs17035506	0.84[ASN][1000 genomes]
rs17035507	0.84[ASN][1000 genomes]
rs17769101	0.90[ASN][1000 genomes]
rs1963249	0.82[ASN][1000 genomes]
rs4580429	0.87[ASN][1000 genomes]
rs4953409	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67716382	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
7	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6742593	NRXN1	cis	parietal	SCAN
rs6742593	CRIPT	cis	cerebellum	SCAN
rs6742593	CRIPT	cis	lymphoblastoid	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46870000-46891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:46884200-46891000	Weak transcription	Pancreas	Pancrea
3	chr2:46884400-46896400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:46884800-46892600	Weak transcription	A549	lung
5	chr2:46885200-46893000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:46888800-46891600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:46889000-46896800	Enhancers	Fetal Muscle Leg	muscle
8	chr2:46889200-46896400	Enhancers	Colon Smooth Muscle	Colon
9	chr2:46889400-46890800	Enhancers	HSMM	muscle
10	chr2:46889400-46891200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:46889400-46891400	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr2:46889400-46891600	Enhancers	Ovary	ovary
13	chr2:46889400-46891800	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr2:46889600-46890600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:46889600-46890600	Enhancers	NHEK	skin
16	chr2:46889600-46890800	Enhancers	NHDF-Ad	bronchial
17	chr2:46889600-46891000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:46889600-46891200	Enhancers	HSMMtube	muscle
19	chr2:46889600-46891800	Enhancers	Fetal Heart	heart
20	chr2:46889600-46891800	Enhancers	Fetal Muscle Trunk	muscle
21	chr2:46889600-46898200	Enhancers	Fetal Stomach	stomach
22	chr2:46889800-46891200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:46889800-46891800	Enhancers	Left Ventricle	heart
24	chr2:46890000-46891200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr2:46890000-46891600	Enhancers	Right Atrium	heart
26	chr2:46890200-46890600	Weak transcription	Psoas Muscle	Psoas
27	chr2:46890200-46890600	Weak transcription	Right Ventricle	heart
28	chr2:46890200-46891000	Enhancers	HMEC	breast
29	chr2:46890200-46891200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr2:46890200-46892400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr2:46890200-46893200	Weak transcription	Fetal Kidney	kidney
32	chr2:46890200-46896400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:46890400-46890600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:46890400-46891000	Enhancers	Osteobl	bone
35	chr2:46890400-46892000	Weak transcription	Fetal Lung	lung
36	chr2:46890400-46894400	Weak transcription	Aorta	Aorta
37	chr2:46890400-46897000	Enhancers	Rectal Smooth Muscle	rectum

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