Variant report

Variant	rs12477228
Chromosome Location	chr2:20618016-20618017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20605791..20608385-chr2:20615767..20618423,2	K562	blood:
2	chr2:20616643..20618657-chr2:20618688..20621631,2	MCF-7	breast:
3	chr2:20611214..20614002-chr2:20617108..20620081,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11901184	0.87[CEU][hapmap];0.84[GIH][hapmap];0.82[LWK][hapmap];0.88[EUR][1000 genomes]
rs12464277	0.88[EUR][1000 genomes]
rs12466143	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12471220	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12471293	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476941	0.80[EUR][1000 genomes]
rs1985318	0.82[EUR][1000 genomes]
rs1985319	0.88[EUR][1000 genomes]
rs2128832	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2128833	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2348705	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs343138	0.81[EUR][1000 genomes]
rs343142	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs343152	0.83[CEU][hapmap];0.84[GIH][hapmap];0.85[EUR][1000 genomes]
rs4666306	0.89[EUR][1000 genomes]
rs4666386	0.84[EUR][1000 genomes]
rs4666387	0.84[EUR][1000 genomes]
rs4666389	0.89[EUR][1000 genomes]
rs4666390	0.89[EUR][1000 genomes]
rs6705947	0.86[EUR][1000 genomes]
rs6734065	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67464308	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67511352	0.88[EUR][1000 genomes]
rs7563890	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs7564799	0.87[EUR][1000 genomes]
rs7564810	0.87[EUR][1000 genomes]
rs7576439	0.88[EUR][1000 genomes]
rs7576806	0.85[EUR][1000 genomes]
rs7603518	0.88[EUR][1000 genomes]
rs7604195	0.83[EUR][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	nsv873716	chr2:20572094-20621404	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12477228	GDF7	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20610400-20621000	Weak transcription	Left Ventricle	heart
2	chr2:20611200-20618200	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:20611200-20618400	Weak transcription	HSMM	muscle
4	chr2:20611600-20618400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:20614200-20618800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:20615600-20618400	Weak transcription	Stomach Mucosa	stomach
7	chr2:20615600-20619000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:20615600-20619000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:20615600-20619600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:20615600-20621000	Weak transcription	Esophagus	oesophagus
11	chr2:20615600-20621000	Weak transcription	NHDF-Ad	bronchial
12	chr2:20615600-20621600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:20615600-20624200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:20615800-20619000	Weak transcription	Placenta	Placenta
15	chr2:20615800-20621400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:20616000-20618800	Weak transcription	HMEC	breast
17	chr2:20616000-20618800	Weak transcription	K562	blood
18	chr2:20616000-20619000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:20616000-20621200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:20616000-20621400	Weak transcription	NHEK	skin
21	chr2:20616200-20618400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:20616200-20619600	Enhancers	Liver	Liver
23	chr2:20616400-20618800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:20617000-20618800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr2:20617000-20621600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr2:20617200-20618200	Enhancers	HepG2	liver
27	chr2:20617200-20618400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:20617200-20618400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:20617200-20618400	Weak transcription	HSMMtube	muscle
30	chr2:20617200-20618800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:20617200-20623400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:20617800-20618400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:20618000-20618800	Enhancers	Adipose Nuclei	Adipose

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