Variant report

Variant	rs7974928
Chromosome Location	chr12:39824971-39824972
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39821875..39824994-chr12:39835535..39837994,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10876868	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs10876876	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs10876972	0.84[CEU][hapmap]
rs10876989	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11171674	0.86[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs11171675	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs11171676	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs11171720	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11171789	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs11171891	0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11171901	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs11171923	0.84[CEU][hapmap]
rs11171938	0.95[CEU][hapmap]
rs11172108	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs11172120	0.84[CEU][hapmap];0.80[MEX][hapmap];0.80[EUR][1000 genomes]
rs11172183	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172235	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11172264	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172282	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11172319	0.81[EUR][1000 genomes]
rs11172320	0.83[EUR][1000 genomes]
rs11172492	0.84[CEU][hapmap]
rs11172541	0.90[EUR][1000 genomes]
rs11172592	0.87[CEU][hapmap]
rs11172650	0.82[EUR][1000 genomes]
rs11836755	0.80[CHB][hapmap]
rs12228767	0.80[MEX][hapmap]
rs12230604	0.95[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs12424345	0.84[CEU][hapmap]
rs1512941	0.81[ASW][hapmap]
rs1567739	0.84[CEU][hapmap];0.80[MEX][hapmap]
rs1828653	0.95[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs2388320	0.84[CEU][hapmap];0.80[MEX][hapmap]
rs3736466	0.81[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap]
rs4320988	0.84[CEU][hapmap]
rs4378431	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4466883	0.83[EUR][1000 genomes]
rs4492858	0.84[CEU][hapmap]
rs4500523	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs4564382	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58240943	0.81[EUR][1000 genomes]
rs58613501	0.80[EUR][1000 genomes]
rs59695906	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60263267	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60900225	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6581188	0.89[EUR][1000 genomes]
rs7137143	0.91[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs73094410	0.81[EUR][1000 genomes]
rs7316073	0.84[CEU][hapmap]
rs7962283	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7965222	0.82[EUR][1000 genomes]
rs7966540	0.86[EUR][1000 genomes]
rs7968837	0.84[CEU][hapmap]
rs7976275	0.81[ASW][hapmap]
rs7979444	0.95[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7974928	KIF21A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39785000-39829200	Weak transcription	K562	blood
2	chr12:39806600-39834200	Weak transcription	Hela-S3	cervix
3	chr12:39808600-39830800	Weak transcription	Fetal Brain Female	brain
4	chr12:39813600-39833400	Weak transcription	Brain Germinal Matrix	brain
5	chr12:39814200-39825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:39814400-39833800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:39816000-39834000	Weak transcription	Left Ventricle	heart
8	chr12:39821400-39835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:39822000-39829800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:39822200-39832200	Weak transcription	A549	lung
11	chr12:39822200-39833000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:39823000-39826000	Enhancers	Liver	Liver
13	chr12:39823200-39825000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:39823600-39825400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:39823600-39829400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:39824000-39832400	Weak transcription	HepG2	liver
17	chr12:39824400-39826000	Enhancers	Fetal Heart	heart
18	chr12:39824600-39825200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:39824600-39825200	Enhancers	Right Ventricle	heart
20	chr12:39824600-39826000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr12:39824600-39826800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:39824800-39825200	Enhancers	Right Atrium	heart

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