Variant report

Variant	rs7527034
Chromosome Location	chr1:180541495-180541496
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180530731..180535452-chr1:180539258..180542430,4	K562	blood:
2	chr1:180541054..180543559-chr1:180545286..180546828,2	K562	blood:
3	chr1:180535652..180538329-chr1:180539867..180543816,3	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10798778	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10914042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10914043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914044	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10914046	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10914047	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2331545	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34569745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4083947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6678305	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7532437	0.80[ASN][1000 genomes]
rs7542168	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9943120	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7527034	NPHS2	cis	cerebellum	SCAN
rs7527034	C1orf220	cis	parietal	SCAN
rs7527034	ANGPTL1	cis	parietal	SCAN
rs7527034	SOAT1	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180536200-180543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:180537400-180541600	Weak transcription	Fetal Intestine Large	intestine
3	chr1:180538600-180543400	Weak transcription	Fetal Brain Female	brain
4	chr1:180539400-180542200	Enhancers	K562	blood
5	chr1:180539600-180542200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:180539600-180542200	Enhancers	HMEC	breast
7	chr1:180539600-180542200	Enhancers	HSMMtube	muscle
8	chr1:180539600-180542200	Enhancers	NHEK	skin
9	chr1:180539600-180546200	Weak transcription	Left Ventricle	heart
10	chr1:180539800-180542000	Weak transcription	Fetal Brain Male	brain
11	chr1:180540000-180541600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:180540000-180541600	Enhancers	NHLF	lung
13	chr1:180540000-180542000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:180540000-180542200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:180540400-180541800	Enhancers	Right Ventricle	heart
16	chr1:180540600-180542200	Enhancers	Esophagus	oesophagus
17	chr1:180540600-180543400	Weak transcription	Fetal Heart	heart
18	chr1:180540600-180543400	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr1:180540800-180542200	Enhancers	Stomach Mucosa	stomach
20	chr1:180540800-180542200	Enhancers	Hela-S3	cervix
21	chr1:180540800-180542800	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:180540800-180543400	Enhancers	Pancreas	Pancrea
23	chr1:180540800-180543600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:180541000-180541600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:180541000-180541800	Enhancers	GM12878-XiMat	blood
26	chr1:180541000-180542200	Enhancers	A549	lung
27	chr1:180541200-180541800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:180541200-180541800	Enhancers	Osteobl	bone
29	chr1:180541200-180542200	Enhancers	Colonic Mucosa	Colon
30	chr1:180541200-180544000	Enhancers	HepG2	liver
31	chr1:180541400-180542000	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:180541400-180542600	Enhancers	Rectal Mucosa Donor 31	rectum

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