Variant report

Variant	rs12330058
Chromosome Location	chr22:31474554-31474555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31358868..31372302-chr22:31474097..31485545,64	MCF-7	breast:
2	chr22:31457775..31462699-chr22:31474304..31478789,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183963	Chromatin interaction
ENSG00000133422	Chromatin interaction
ENSG00000253352	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10427701	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10854603	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11705177	0.97[ASN][1000 genomes]
rs11705250	0.97[ASN][1000 genomes]
rs11705313	0.97[ASN][1000 genomes]
rs11705396	0.86[ASN][1000 genomes]
rs12157450	0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12157641	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs12158536	0.85[YRI][hapmap]
rs12165471	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168052	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12170984	0.97[ASN][1000 genomes]
rs13053618	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13057068	0.97[ASN][1000 genomes]
rs2006301	0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs35060453	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753456	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs5994365	0.90[ASN][1000 genomes]
rs5994366	1.00[JPT][hapmap]
rs5994368	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997863	0.97[ASN][1000 genomes]
rs5997864	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs5997866	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs5997871	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5997872	0.85[ASN][1000 genomes]
rs715297	1.00[JPT][hapmap]
rs7284593	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7285683	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7291565	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7292038	0.97[ASN][1000 genomes]
rs7292982	0.84[ASN][1000 genomes]
rs736901	0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs9619166	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9619167	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9621175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv20214	chr22:31461316-31474644	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv914975	chr22:31466083-31514477	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv979668	chr22:31473892-31475436	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12330058	MORC2-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31465800-31475000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr22:31469800-31476400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr22:31469800-31476400	Weak transcription	HUVEC	blood vessel
4	chr22:31470200-31475000	Weak transcription	Spleen	Spleen
5	chr22:31471400-31476600	Weak transcription	Left Ventricle	heart
6	chr22:31472000-31476400	Weak transcription	HSMMtube	muscle
7	chr22:31472200-31475400	Weak transcription	Lung	lung
8	chr22:31472200-31476200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr22:31472200-31476400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:31472400-31475000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr22:31472400-31475000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr22:31472400-31475200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr22:31472400-31476400	Weak transcription	Ovary	ovary
14	chr22:31472400-31476600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr22:31472400-31476600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr22:31472400-31476600	Weak transcription	Psoas Muscle	Psoas
17	chr22:31472600-31475000	Weak transcription	Colonic Mucosa	Colon
18	chr22:31472600-31476200	Weak transcription	Fetal Lung	lung
19	chr22:31472600-31476400	Weak transcription	Adipose Nuclei	Adipose
20	chr22:31472600-31476400	Weak transcription	Right Ventricle	heart
21	chr22:31472600-31476400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr22:31472600-31476400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr22:31472600-31476400	Weak transcription	NHDF-Ad	bronchial
24	chr22:31472600-31476600	Weak transcription	Right Atrium	heart
25	chr22:31472600-31476600	Weak transcription	NHLF	lung
26	chr22:31473600-31476400	Enhancers	Fetal Intestine Large	intestine
27	chr22:31473800-31474600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr22:31473800-31475400	Enhancers	Placenta	Placenta
29	chr22:31473800-31476400	Enhancers	Fetal Intestine Small	intestine
30	chr22:31473800-31476400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr22:31474000-31475000	Weak transcription	Pancreas	Pancrea
32	chr22:31474000-31475200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr22:31474200-31474600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr22:31474200-31474600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr22:31474200-31474600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr22:31474200-31474600	Enhancers	HSMM	muscle
37	chr22:31474200-31474600	Enhancers	Osteobl	bone
38	chr22:31474200-31474800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr22:31474200-31474800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr22:31474200-31474800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr22:31474200-31474800	Enhancers	HepG2	liver
42	chr22:31474200-31475000	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr22:31474200-31475000	Enhancers	NHEK	skin
44	chr22:31474200-31475200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr22:31474200-31475400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr22:31474200-31476400	Enhancers	Fetal Muscle Leg	muscle
47	chr22:31474200-31476600	Enhancers	Fetal Stomach	stomach
48	chr22:31474400-31474600	Enhancers	Esophagus	oesophagus
49	chr22:31474400-31474600	Enhancers	HMEC	breast
50	chr22:31474400-31474800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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