Variant report

Variant	rs7974410
Chromosome Location	chr12:47594463-47594464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47591993..47593635-chr12:47593815..47595761,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10881077	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10881079	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11183779	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs11183783	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11183795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183796	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183799	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12370192	0.84[ASW][hapmap]
rs12370622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554693	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17222290	0.84[ASW][hapmap]
rs17821774	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17822189	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1917657	0.84[ASW][hapmap]
rs2004683	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004684	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2111903	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408718	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768142	0.84[ASW][hapmap]
rs4768144	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4768782	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55711758	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55849521	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712100	1.00[CHB][hapmap]
rs73110240	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs732523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs855146	1.00[CHB][hapmap]
rs855147	1.00[CHB][hapmap]
rs873935	1.00[CHB][hapmap]
rs952967	0.84[ASW][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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7974410	C12orf68	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47583200-47628600	Weak transcription	Aorta	Aorta
2	chr12:47584000-47600600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:47584800-47597200	Weak transcription	Primary B cells from cord blood	blood
4	chr12:47584800-47605800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:47585400-47600400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:47585600-47599800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:47585800-47601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:47588200-47599600	Weak transcription	Fetal Thymus	thymus
9	chr12:47588600-47597800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:47588600-47599800	Weak transcription	Spleen	Spleen
11	chr12:47589400-47598400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:47589600-47597200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:47589600-47599200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:47590200-47597600	Weak transcription	Primary T cells from cord blood	blood
15	chr12:47590600-47594800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:47591400-47597200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr12:47591600-47597600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr12:47591600-47598200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:47591800-47594800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:47592200-47595800	Weak transcription	A549	lung
21	chr12:47592400-47597800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:47593200-47596400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:47593400-47594800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:47593800-47594600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:47594000-47594600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr12:47594000-47594600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr12:47594200-47595600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:47594400-47595200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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