Variant report

Variant	rs2609954
Chromosome Location	chr2:30871808-30871809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30870789..30872377-chr2:30883033..30885539,2	K562	blood:
2	chr2:30869841..30871962-chr2:30899360..30901880,2	MCF-7	breast:
3	chr2:30864804..30866571-chr2:30870628..30873251,2	MCF-7	breast:
4	chr2:30867045..30872289-chr2:30881194..30886841,8	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10167083	0.86[CEU][hapmap]
rs10175399	0.93[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs10183928	0.85[CEU][hapmap]
rs12053428	0.86[CEU][hapmap]
rs12468064	0.86[CEU][hapmap]
rs1252625	0.93[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs1252631	0.86[CEU][hapmap]
rs1252646	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs1252651	0.86[CEU][hapmap]
rs1447193	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1525062	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs1869423	0.86[CEU][hapmap];0.94[GIH][hapmap]
rs1869424	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs1975555	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs2121600	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs2123753	0.86[CEU][hapmap]
rs2177698	0.86[CEU][hapmap]
rs2593442	0.86[CEU][hapmap]
rs2593457	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2593474	0.86[CEU][hapmap];0.94[GIH][hapmap]
rs2602767	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs2602808	0.86[CEU][hapmap];0.89[GIH][hapmap]
rs2609917	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs2609945	0.89[GIH][hapmap];1.00[JPT][hapmap]
rs2609951	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609960	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4952147	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs6731031	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs6740440	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs7583211	0.86[CEU][hapmap]
rs7591110	0.86[CEU][hapmap]
rs7592355	0.86[CEU][hapmap]
rs829563	0.85[CEU][hapmap]
rs829564	0.86[CEU][hapmap]
rs829565	0.86[CEU][hapmap]
rs829574	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs829575	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs829582	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs829618	0.93[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs829619	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs829620	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs829622	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829630	0.86[CEU][hapmap]
rs829631	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs829632	0.86[CEU][hapmap]
rs829634	0.93[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs829641	0.93[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs829642	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs829646	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs829653	0.86[CEU][hapmap]
rs829654	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829655	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs829659	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs829661	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs829662	0.82[EUR][1000 genomes]
rs829663	0.82[EUR][1000 genomes]
rs829664	0.85[CEU][hapmap];0.97[GIH][hapmap]
rs829669	0.93[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs829671	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs829672	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs829673	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs829675	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs829677	0.93[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs829679	0.93[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs829680	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs829681	0.86[CEU][hapmap]
rs829682	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs829684	0.86[CEU][hapmap]
rs844194	0.93[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs860487	0.85[CEU][hapmap]
rs866680	0.85[CEU][hapmap]
rs9309680	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv581266	chr2:30864789-30874229	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2609954	YPEL5	cis	parietal	SCAN
rs2609954	EMILIN1	cis	parietal	SCAN
rs2609954	FOSL2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30841800-30872200	Weak transcription	Spleen	Spleen
2	chr2:30845600-30877800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:30845800-30877800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:30850200-30874600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:30850400-30874600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:30853200-30872000	Weak transcription	NHDF-Ad	bronchial
7	chr2:30859600-30872000	Weak transcription	Fetal Stomach	stomach
8	chr2:30860400-30878200	Weak transcription	NHLF	lung
9	chr2:30861400-30876800	Weak transcription	Fetal Heart	heart
10	chr2:30861600-30872200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:30863600-30882200	Weak transcription	Ovary	ovary
12	chr2:30864000-30872000	Weak transcription	Right Ventricle	heart
13	chr2:30864000-30874800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:30864200-30872200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:30864800-30875200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:30864800-30876600	Weak transcription	Osteobl	bone
17	chr2:30865000-30872200	Weak transcription	Aorta	Aorta
18	chr2:30865000-30875200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:30865200-30872000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:30865200-30872200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:30865200-30873000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:30865200-30877000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:30865200-30878200	Weak transcription	A549	lung
24	chr2:30865600-30872000	Weak transcription	Fetal Intestine Small	intestine
25	chr2:30866800-30872200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:30869000-30872000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:30869200-30878000	Weak transcription	Psoas Muscle	Psoas
28	chr2:30871400-30873600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:30871600-30872400	Enhancers	Lung	lung
30	chr2:30871600-30873000	Enhancers	Fetal Muscle Leg	muscle
31	chr2:30871800-30872000	Enhancers	Colon Smooth Muscle	Colon
32	chr2:30871800-30872200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:30871800-30872400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:30871800-30872400	Enhancers	Left Ventricle	heart
35	chr2:30871800-30872400	Enhancers	Stomach Smooth Muscle	stomach
36	chr2:30871800-30872600	Enhancers	HSMMtube	muscle

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