Variant report

Variant	rs7979444
Chromosome Location	chr12:39805978-39805979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39804679..39806522-chr12:39811533..39813150,2	K562	blood:
2	chr12:39803978..39806554-chr12:39812297..39814697,2	MCF-7	breast:
3	chr12:39804581..39806388-chr12:39821812..39823553,2	K562	blood:
4	chr12:39804413..39806857-chr12:39807005..39809707,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10876868	0.94[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs10876876	0.94[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs10876886	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10876972	0.88[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs10876989	0.89[EUR][1000 genomes]
rs11171674	0.88[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs11171675	0.88[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs11171676	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]
rs11171720	0.88[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs11171789	0.82[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs11171891	0.82[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs11171901	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11171923	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs11171938	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11172108	0.83[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap]
rs11172120	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11172183	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172235	0.91[EUR][1000 genomes]
rs11172264	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11172282	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs11172492	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs11172541	0.83[EUR][1000 genomes]
rs11172592	0.82[CEU][hapmap];0.94[JPT][hapmap]
rs11172661	0.95[JPT][hapmap]
rs11830643	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs11836755	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12228767	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs12230604	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12424345	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1512936	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1567739	0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs17127019	0.81[ASN][1000 genomes]
rs1828653	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2388320	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs3736466	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs4284427	0.88[JPT][hapmap]
rs4320988	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs4378431	0.81[EUR][1000 genomes]
rs4492858	0.88[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4500523	0.83[CEU][hapmap];0.95[JPT][hapmap]
rs4564382	0.92[EUR][1000 genomes]
rs57756176	0.82[ASN][1000 genomes]
rs57833783	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs59695906	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60263267	0.82[EUR][1000 genomes]
rs60792848	0.81[ASN][1000 genomes]
rs60900225	0.91[EUR][1000 genomes]
rs6581188	0.82[EUR][1000 genomes]
rs7137143	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs7316073	0.90[JPT][hapmap]
rs7953548	0.81[ASN][1000 genomes]
rs7962283	0.87[CEU][hapmap]
rs7964447	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7966540	0.83[EUR][1000 genomes]
rs7968837	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs7971515	0.80[ASN][1000 genomes]
rs7974928	0.95[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs7979329	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7979444	KIF21A	cis	cerebellum	SCAN
rs7979444	KIF21A	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
2	chr12:39785000-39829200	Weak transcription	K562	blood
3	chr12:39790000-39816200	Weak transcription	Right Ventricle	heart
4	chr12:39794200-39824800	Weak transcription	Right Atrium	heart
5	chr12:39795400-39816600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:39797600-39812000	Weak transcription	HMEC	breast
7	chr12:39798200-39807000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:39798200-39809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:39800800-39806000	Weak transcription	Placenta	Placenta
10	chr12:39800800-39807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:39800800-39807400	Weak transcription	GM12878-XiMat	blood
12	chr12:39800800-39807800	Weak transcription	Ovary	ovary
13	chr12:39800800-39812000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:39800800-39814800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:39801000-39807200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:39801000-39808000	Weak transcription	Brain Anterior Caudate	brain
17	chr12:39801000-39815800	Weak transcription	Psoas Muscle	Psoas
18	chr12:39801200-39808200	Weak transcription	A549	lung
19	chr12:39801400-39807000	Weak transcription	Brain Substantia Nigra	brain
20	chr12:39801400-39807400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:39801600-39811000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:39802000-39811800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:39802400-39809200	Weak transcription	Left Ventricle	heart
24	chr12:39802400-39816000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:39802800-39806800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:39803400-39807200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:39803800-39806000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:39804000-39808200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:39804000-39811800	Weak transcription	Adipose Nuclei	Adipose
30	chr12:39804400-39809000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:39804800-39806400	Strong transcription	Fetal Brain Female	brain
32	chr12:39805000-39806400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:39805000-39807200	Weak transcription	Fetal Stomach	stomach
34	chr12:39805000-39807800	Weak transcription	Fetal Heart	heart
35	chr12:39805200-39806400	Strong transcription	Brain Germinal Matrix	brain
36	chr12:39805200-39806600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:39805200-39807400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:39805200-39811800	Weak transcription	HepG2	liver
39	chr12:39805400-39806400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:39805400-39807400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr12:39805600-39806400	Strong transcription	Liver	Liver
42	chr12:39805800-39806000	Strong transcription	Fetal Intestine Small	intestine

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