Variant report

Variant	rs2111201
Chromosome Location	chr7:107965942-107965943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107955015..107957459-chr7:107963418..107966174,2	K562	blood:
2	chr7:107964856..107967775-chr7:107967931..107970381,3	MCF-7	breast:
3	chr7:107962380..107965223-chr7:107965724..107968731,3	K562	blood:
4	chr7:107964764..107967252-chr7:108095497..108097482,2	MCF-7	breast:
5	chr7:107965337..107967353-chr7:107989055..107990953,2	K562	blood:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12671060	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13225168	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13242382	1.00[ASN][1000 genomes]
rs2111202	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267883	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs2267884	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2267887	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs4142284	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4727706	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7800100	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs9649300	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1019059	chr7:107935905-107995523	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1021783	chr7:107935905-107998281	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv2761354	chr7:107935905-107998293	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1031824	chr7:107935905-108006038	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv1017288	chr7:107939739-108000837	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2111201	LRRN3	cis	cerebellum	SCAN
rs2111201	CDHR3	cis	cerebellum	SCAN
rs2111201	NME3	trans	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107953400-107968600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:107954000-107967200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:107962600-107967400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:107963000-107966800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:107963400-107972400	Weak transcription	Brain Anterior Caudate	brain
6	chr7:107963600-107971200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:107964000-107967000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:107964200-107966000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:107964200-107966400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:107964400-107968600	Weak transcription	Fetal Lung	lung
11	chr7:107964600-107970200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:107964800-107966800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:107964800-107967200	Weak transcription	Brain Angular Gyrus	brain
14	chr7:107965000-107967400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:107965200-107966400	Enhancers	A549	lung
16	chr7:107965200-107967400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:107965200-107968400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:107965200-107970000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:107965600-107967000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:107965600-107967200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:107965600-107967400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:107965600-107967400	Weak transcription	Pancreas	Pancrea
23	chr7:107965800-107966800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:107965800-107967000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:107965800-107967000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:107965800-107967400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr7:107965800-107968600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:107965800-107968800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:107965800-107971000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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