Variant report

Variant	rs12986437
Chromosome Location	chr2:20204690-20204691
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20099721..20101368-chr2:20204158..20205910,2	K562	blood:
2	chr2:20194768..20196948-chr2:20202160..20205024,2	K562	blood:
3	chr2:20203665..20207469-chr2:20209736..20214726,5	MCF-7	breast:
4	chr2:20203402..20205904-chr2:20205994..20208147,2	MCF-7	breast:
5	chr2:20188602..20191766-chr2:20204187..20206956,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132031	Chromatin interaction
ENSG00000118965	Chromatin interaction
ENSG00000227210	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1056233	0.89[CEU][hapmap];0.92[GIH][hapmap]
rs1115275	0.89[CEU][hapmap]
rs11680554	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11681705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683973	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs11688098	0.85[AMR][1000 genomes]
rs11693384	0.89[CEU][hapmap]
rs11694821	0.88[CEU][hapmap]
rs12988913	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs12990087	0.89[CEU][hapmap];0.92[GIH][hapmap]
rs12995324	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12996974	0.88[CEU][hapmap]
rs13005512	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13011870	0.80[AMR][1000 genomes]
rs13035048	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs1370585	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap]
rs16987220	0.89[CEU][hapmap]
rs16987257	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes]
rs17695872	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1921731	0.89[CEU][hapmap]
rs2028208	0.94[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes]
rs28452699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34400777	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs34595677	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34741640	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35307726	0.82[AMR][1000 genomes]
rs35973216	0.80[AMR][1000 genomes]
rs4294960	0.89[CEU][hapmap];0.92[GIH][hapmap]
rs66482567	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6706311	0.82[AMR][1000 genomes]
rs6720011	0.88[CEU][hapmap]
rs67724270	0.82[AMR][1000 genomes]
rs67915887	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721932	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs721933	0.94[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73214266	0.81[AMR][1000 genomes]
rs957614	0.89[CEU][hapmap];0.92[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12986437	RDH14	cis	cerebellum	SCAN
rs12986437	WDR35	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20190400-20207400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:20190600-20211400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:20190800-20205000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:20190800-20208400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:20191000-20211200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:20191400-20208000	Weak transcription	A549	lung
7	chr2:20200000-20206800	Weak transcription	HSMMtube	muscle
8	chr2:20200200-20211800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:20201800-20211400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:20201800-20212400	Weak transcription	Gastric	stomach
11	chr2:20202000-20210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:20202400-20210200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:20203000-20205600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:20203000-20206400	Genic enhancers	HepG2	liver
15	chr2:20203800-20206800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:20204200-20205600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:20204400-20205200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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