Variant report

Variant	rs10877990
Chromosome Location	chr12:40429582-40429583
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	chr12:40427544..40429854-chr12:40484526..40486904,2	MCF-7	breast:
2	chr12:40428243..40430877-chr12:40432067..40435027,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1005956	0.83[JPT][hapmap]
rs10506140	0.83[JPT][hapmap]
rs10747971	0.84[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs10747989	0.93[YRI][hapmap]
rs10784338	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784353	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10784356	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10784359	0.90[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10784369	0.94[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10877891	0.92[JPT][hapmap]
rs10878031	0.82[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10878049	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10878089	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs11174609	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs11174670	0.89[ASN][1000 genomes]
rs11174809	0.85[ASN][1000 genomes]
rs11174812	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11174813	0.85[ASN][1000 genomes]
rs11175024	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs12813098	0.92[JPT][hapmap]
rs12823555	0.92[JPT][hapmap]
rs1482281	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs1586038	0.88[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1600866	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1813122	0.92[JPT][hapmap];0.82[YRI][hapmap]
rs2128275	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2128277	0.92[JPT][hapmap]
rs2404352	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2896825	0.88[CEU][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3925535	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4625545	0.83[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768200	0.90[JPT][hapmap]
rs4768204	0.83[JPT][hapmap]
rs530602	0.92[JPT][hapmap]
rs550669	0.92[JPT][hapmap]
rs6581504	0.92[JPT][hapmap]
rs6650226	0.92[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs7139216	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs716268	0.92[JPT][hapmap]
rs7313209	0.92[CEU][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7313231	0.82[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7953129	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7954875	0.89[ASN][1000 genomes]
rs7959498	0.88[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7960662	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7964150	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs7970812	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs9669240	0.92[JPT][hapmap]

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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10877990	KIF21A	Cis_1M	lymphoblastoid	RTeQTL
rs10877990	SLC2A13	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40405400-40445200	Weak transcription	K562	blood
3	chr12:40416600-40441800	Weak transcription	Ovary	ovary
4	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
5	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
6	chr12:40425600-40429800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:40427800-40430000	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr12:40428000-40429600	Enhancers	A549	lung
10	chr12:40428000-40436400	Weak transcription	Fetal Intestine Large	intestine
11	chr12:40428000-40452600	Weak transcription	Fetal Intestine Small	intestine
12	chr12:40429000-40433400	Weak transcription	Fetal Lung	lung
13	chr12:40429400-40441000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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