Variant report

Variant	rs11810473
Chromosome Location	chr1:226403979-226403980
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226401377..226404931-chr1:226406831..226410956,4	MCF-7	breast:
2	chr1:226373756..226375724-chr1:226401681..226404608,2	K562	blood:
3	chr1:226403910..226406210-chr1:226410473..226412333,2	K562	blood:
4	chr1:226403447..226405521-chr1:226495731..226497298,2	K562	blood:
5	chr1:226403012..226406009-chr1:226466558..226469360,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185155	Chromatin interaction
ENSG00000182827	Chromatin interaction
ENSG00000183814	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12122761	1.00[ASW][hapmap];0.82[GIH][hapmap];0.81[AFR][1000 genomes]
rs12133895	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap]
rs3845509	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2829936	chr1:226375267-226488826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv873233	chr1:226385623-226508645	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11810473	GJC2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226375200-226411000	Weak transcription	Right Atrium	heart
2	chr1:226399000-226411200	Weak transcription	Gastric	stomach
3	chr1:226400000-226404400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr1:226401000-226410800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:226402400-226404000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:226402400-226405600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:226402400-226405600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:226402800-226404200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr1:226402800-226404200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr1:226402800-226404200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:226403000-226404000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:226403200-226404000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:226403200-226404600	Enhancers	K562	blood
14	chr1:226403200-226404800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:226403400-226407800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:226403400-226408000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:226403400-226408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:226403400-226410800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:226403600-226404000	Weak transcription	HepG2	liver
20	chr1:226403600-226410800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:226403800-226404200	Enhancers	Stomach Mucosa	stomach
22	chr1:226403800-226404400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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