Variant report

Variant	rs11972414
Chromosome Location	chr7:128344283-128344284
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128343789..128345525-chr7:128387632..128390357,2	K562	blood:
2	chr7:128336358..128338918-chr7:128343519..128346350,2	K562	blood:
3	chr7:128343745..128346373-chr7:128352660..128354319,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201041	Chromatin interaction
ENSG00000252866	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1003241	0.81[YRI][hapmap]
rs10253936	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11972335	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11973846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11979987	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12668292	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12672216	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1450875	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17169357	0.81[YRI][hapmap]
rs1839595	0.85[EUR][1000 genomes]
rs2290229	0.85[YRI][hapmap]
rs2402932	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4728128	0.81[YRI][hapmap]
rs4731484	0.84[YRI][hapmap]
rs4731485	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4731503	0.81[YRI][hapmap]
rs55854844	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56010148	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59475830	0.85[EUR][1000 genomes]
rs59955357	0.85[EUR][1000 genomes]
rs61031958	0.84[EUR][1000 genomes]
rs62481886	0.85[EUR][1000 genomes]
rs62481894	0.85[EUR][1000 genomes]
rs62481898	0.85[EUR][1000 genomes]
rs62481925	0.81[EUR][1000 genomes]
rs62481947	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6949056	0.85[CHB][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap]
rs6969554	0.81[YRI][hapmap]
rs73236051	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7797745	0.81[YRI][hapmap]
rs9689994	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9690750	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1016979	chr7:128333070-128534438	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	esv3379823	chr7:128343907-128344299	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11972414	RP11-274B21.4	cis	Whole Blood	GTEx
rs11972414	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs11972414	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs11972414	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs11972414	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs11972414	RP11-274B21.1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128338000-128346000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr7:128338600-128349000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:128339000-128358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:128341200-128346000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:128341800-128344800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr7:128341800-128346000	Weak transcription	HMEC	breast
7	chr7:128342000-128344600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:128343400-128345000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:128343600-128345200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:128343600-128345600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:128343800-128345400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr7:128343800-128345400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:128343800-128345800	Weak transcription	Right Atrium	heart
14	chr7:128344000-128344600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:128344000-128345400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr7:128344000-128346200	Weak transcription	Spleen	Spleen
17	chr7:128344000-128348200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:128344000-128349000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:128344200-128344400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr7:128344200-128344600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:128344200-128345000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:128344200-128348600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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