Variant report

Variant	rs2224873
Chromosome Location	chr1:197645449-197645450
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197644483..197647407-chr1:197649632..197652293,2	K562	blood:
2	chr1:197623895..197625439-chr1:197644828..197646522,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10737693	0.91[EUR][1000 genomes]
rs11583319	0.85[TSI][hapmap]
rs11588864	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12117045	0.83[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12131588	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12141028	0.94[MEX][hapmap];0.88[TSI][hapmap]
rs1539414	0.88[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs16841842	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16841904	0.94[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs16841912	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs17641524	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2477077	0.88[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs2488389	0.94[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs2488393	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2488397	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2488398	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs2488401	0.88[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4316387	0.84[EUR][1000 genomes]
rs6682968	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv873077	chr1:197615391-197698103	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2224873	RGS2	cis	parietal	SCAN
rs2224873	DENND1B	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197640800-197647000	Weak transcription	Small Intestine	intestine
2	chr1:197640800-197657600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:197642800-197645800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:197642800-197646800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:197643200-197645600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:197643800-197646800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:197644000-197656000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:197644200-197645600	Enhancers	Fetal Brain Female	brain
9	chr1:197644200-197645800	Enhancers	Fetal Brain Male	brain
10	chr1:197644400-197645600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:197644600-197645600	Enhancers	Fetal Heart	heart
12	chr1:197644600-197646400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:197645000-197645600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr1:197645000-197645600	Enhancers	Dnd41	blood
15	chr1:197645000-197646400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:197645000-197651800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:197645000-197652600	Weak transcription	Left Ventricle	heart
18	chr1:197645200-197645600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:197645200-197645600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr1:197645200-197645600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr1:197645200-197645800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:197645200-197646600	Enhancers	K562	blood
23	chr1:197645200-197647000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:197645200-197661000	Weak transcription	Esophagus	oesophagus
25	chr1:197645400-197645600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:197645400-197645600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:197645400-197645600	Enhancers	Adipose Nuclei	Adipose
28	chr1:197645400-197645600	Enhancers	Liver	Liver
29	chr1:197645400-197645600	Enhancers	NHDF-Ad	bronchial
30	chr1:197645400-197645600	Enhancers	Osteobl	bone
31	chr1:197645400-197645800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:197645400-197646400	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr1:197645400-197646600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:197645400-197647000	Weak transcription	Right Atrium	heart
35	chr1:197645400-197655600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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