Variant report

Variant	rs11561915
Chromosome Location	chr7:147609377-147609378
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11561916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761543	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11771110	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11980029	0.93[JPT][hapmap]
rs12533758	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13225365	0.85[LWK][hapmap];0.82[YRI][hapmap]
rs13234998	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13235220	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs17237331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2215798	0.93[JPT][hapmap]
rs2538964	0.89[CEU][hapmap]
rs2538973	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs2708244	0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2708259	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2710101	1.00[CEU][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs2710103	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2710106	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2710109	0.94[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs34126004	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34902210	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57708946	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58175733	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946545	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs7794222	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11561915	C7orf29	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147601200-147609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:147606600-147610200	Enhancers	Adipose Nuclei	Adipose
3	chr7:147607000-147612400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:147607200-147612200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:147607200-147612600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:147608200-147609800	Enhancers	Primary hematopoietic stem cells	blood
7	chr7:147608200-147609800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:147608200-147609800	Enhancers	Fetal Lung	lung
9	chr7:147608200-147610000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr7:147608200-147610000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr7:147608200-147610000	Enhancers	Brain Substantia Nigra	brain
12	chr7:147608400-147609600	Enhancers	Psoas Muscle	Psoas
13	chr7:147608600-147612200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:147608600-147612400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:147608800-147609600	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr7:147609000-147611000	Enhancers	Fetal Muscle Leg	muscle
17	chr7:147609000-147612200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:147609200-147609600	Enhancers	Colonic Mucosa	Colon
19	chr7:147609200-147609600	Enhancers	Fetal Muscle Trunk	muscle
20	chr7:147609200-147609600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr7:147609200-147610000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:147609200-147611000	Enhancers	Rectal Mucosa Donor 31	rectum

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