Variant report

Variant	rs7304747
Chromosome Location	chr12:117251610-117251611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117251106..117253026-chr12:117352953..117355547,2	MCF-7	breast:
2	chr12:117217330..117219094-chr12:117250590..117252479,2	K562	blood:
3	chr12:117246891..117249993-chr12:117250425..117253317,3	K562	blood:
4	chr12:117245789..117252962-chr12:117254340..117258603,11	K562	blood:
5	chr12:117249993..117252950-chr12:117255244..117258293,4	MCF-7	breast:
6	chr12:117248703..117251842-chr12:117252978..117255376,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10047539	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs10735096	0.92[CHD][hapmap]
rs10735097	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735098	0.90[CEU][hapmap];0.85[TSI][hapmap]
rs10774887	0.92[CHD][hapmap]
rs10774889	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774890	0.80[CEU][hapmap]
rs10850715	0.92[CHD][hapmap]
rs10850722	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850723	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495933	0.80[CEU][hapmap]
rs2393084	0.81[CHD][hapmap]
rs2393107	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393108	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs3926590	0.82[CHD][hapmap]
rs4238048	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4432105	0.84[ASN][1000 genomes]
rs4480639	0.81[EUR][1000 genomes]
rs4767449	0.92[CHD][hapmap]
rs4767454	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767457	0.80[CEU][hapmap]
rs4767458	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767460	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs4767462	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4767463	0.81[ASN][1000 genomes]
rs4767466	0.84[ASN][1000 genomes]
rs4767470	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6490093	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490095	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7314309	0.92[CHD][hapmap]
rs7314377	1.00[CHB][hapmap]
rs7953141	1.00[YRI][hapmap]
rs7980144	0.84[CHD][hapmap]
rs903773	0.84[ASN][1000 genomes]
rs924072	0.80[CEU][hapmap]
rs924075	0.90[CEU][hapmap]
rs924078	0.90[CEU][hapmap]
rs987560	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7304747	RNFT2	cis	parietal	SCAN
rs7304747	MED13L	cis	parietal	SCAN
rs7304747	TBX5	cis	cerebellum	SCAN
rs7304747	MAPKAPK5	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117198000-117256200	Weak transcription	Hela-S3	cervix
2	chr12:117225200-117256200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:117228400-117256400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:117229200-117256200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:117237000-117256200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:117237200-117256200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:117237200-117256200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:117237800-117256000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:117237800-117256200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:117238000-117256200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:117238000-117256200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:117238400-117255600	Enhancers	Fetal Thymus	thymus
13	chr12:117242000-117256200	Weak transcription	GM12878-XiMat	blood
14	chr12:117242200-117256000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:117247000-117255800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:117247000-117256200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:117247200-117256000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:117248200-117256200	Weak transcription	Brain Germinal Matrix	brain
19	chr12:117249000-117256200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:117249400-117256200	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:117250000-117252000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:117250200-117251800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:117250600-117251800	Enhancers	HMEC	breast
24	chr12:117250600-117252000	Enhancers	NHEK	skin
25	chr12:117251000-117251800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:117251200-117256000	Weak transcription	HepG2	liver
27	chr12:117251200-117256200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:117251400-117251800	Weak transcription	Primary B cells from cord blood	blood
29	chr12:117251400-117256200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:117251600-117254600	Enhancers	Thymus	Thymus

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