Variant report

Variant	rs7373994
Chromosome Location	chr3:46701114-46701115
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46694367..46696784-chr3:46700533..46702461,2	K562	blood:
2	chr3:46700787..46702922-chr3:46710281..46712322,2	K562	blood:
3	chr3:46699829..46702382-chr3:46705244..46707445,2	K562	blood:
4	chr3:46698830..46701329-chr3:46704770..46706744,2	K562	blood:
5	chr3:46700528..46705296-chr3:46732661..46735807,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178038	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11130099	0.89[ASN][1000 genomes]
rs11130102	0.85[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11710586	0.95[ASN][1000 genomes]
rs11719679	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs11922418	0.91[ASN][1000 genomes]
rs12491236	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs12491294	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs13083665	0.89[ASN][1000 genomes]
rs1402148	0.86[ASN][1000 genomes]
rs1520488	0.86[ASN][1000 genomes]
rs1520489	0.86[ASN][1000 genomes]
rs1581325	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1607737	0.86[ASN][1000 genomes]
rs34000414	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34063921	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34820891	0.94[ASN][1000 genomes]
rs4234464	0.87[ASN][1000 genomes]
rs4683256	0.86[ASN][1000 genomes]
rs4683260	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4683271	0.87[ASN][1000 genomes]
rs59048074	0.81[EUR][1000 genomes]
rs6442011	0.85[ASN][1000 genomes]
rs6442012	0.87[ASN][1000 genomes]
rs6808214	0.86[ASN][1000 genomes]
rs7643859	0.82[ASN][1000 genomes]
rs7644072	0.82[ASN][1000 genomes]
rs877680	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs877681	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs950190	0.86[ASN][1000 genomes]
rs9845998	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7373994	LRRC2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46693400-46701800	Weak transcription	Right Atrium	heart
2	chr3:46698000-46707600	Weak transcription	Gastric	stomach
3	chr3:46699000-46701400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:46699000-46701800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:46699000-46702000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:46699400-46701400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:46699400-46701600	Weak transcription	NHDF-Ad	bronchial
8	chr3:46700400-46704200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:46700400-46704800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:46700400-46705400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:46700400-46705800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:46700400-46705800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:46700600-46701200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr3:46700600-46701200	Enhancers	HSMMtube	muscle
15	chr3:46700600-46702600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:46700600-46703000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:46700600-46703000	Enhancers	NHEK	skin
18	chr3:46700600-46704200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr3:46700600-46705000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:46700600-46705000	Enhancers	HMEC	breast
21	chr3:46700600-46705400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:46700600-46705600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:46700800-46701200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:46700800-46703000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:46700800-46704000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:46700800-46705400	Enhancers	Placenta	Placenta
27	chr3:46700800-46710400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr3:46701000-46702200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:46701000-46703000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:46701000-46704400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:46701000-46704600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:46701000-46705000	Enhancers	H9 Cell Line	embryonic stem cell

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