Variant report

Variant	rs2609955
Chromosome Location	chr2:30872022-30872023
allele	C/T
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	chr2:30869127..30871765-chr2:30871926..30874749,3	K562	blood:
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: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10167083	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs10175399	0.93[CEU][hapmap]
rs10183928	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs10865520	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1096109	0.88[EUR][1000 genomes]
rs11127278	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12053428	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs12468064	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1252625	0.93[CEU][hapmap]
rs1252631	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs1252640	0.88[EUR][1000 genomes]
rs1252646	0.93[CEU][hapmap];0.97[GIH][hapmap]
rs1252651	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs12999917	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13024015	0.93[ASN][1000 genomes]
rs1447186	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1447187	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470533	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470534	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470536	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525062	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1869423	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1869424	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1869429	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975555	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2121600	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2123753	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs2177698	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2266377	0.82[EUR][1000 genomes]
rs2593440	0.92[EUR][1000 genomes]
rs2593442	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593443	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593448	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593452	0.91[EUR][1000 genomes]
rs2593455	0.89[EUR][1000 genomes]
rs2593458	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593459	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2593460	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593461	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593464	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593466	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593474	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2602767	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2602780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602783	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602785	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602786	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602789	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602790	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602791	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602792	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602798	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2602799	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602806	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2602807	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602808	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2609917	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2609924	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2609925	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2609926	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2609943	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2609945	0.93[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2609950	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2609952	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609956	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609958	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862977	0.88[EUR][1000 genomes]
rs4952147	0.93[CEU][hapmap];0.97[GIH][hapmap]
rs62142163	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6731031	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6740440	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6759011	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7566983	0.88[EUR][1000 genomes]
rs7572318	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7583211	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7591110	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7592355	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs7605994	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7606200	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829563	1.00[CEU][hapmap]
rs829564	1.00[CEU][hapmap]
rs829565	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs829574	0.86[CEU][hapmap]
rs829575	0.93[CEU][hapmap];0.94[GIH][hapmap]
rs829582	0.86[CEU][hapmap]
rs829616	0.89[EUR][1000 genomes]
rs829617	0.89[EUR][1000 genomes]
rs829618	0.93[CEU][hapmap];0.97[GIH][hapmap]
rs829619	0.86[CEU][hapmap]
rs829620	0.86[CEU][hapmap]
rs829622	0.93[CEU][hapmap]
rs829629	0.84[EUR][1000 genomes]
rs829630	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs829631	0.86[CEU][hapmap]
rs829632	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs829634	0.93[CEU][hapmap]
rs829635	0.89[EUR][1000 genomes]
rs829637	0.88[EUR][1000 genomes]
rs829641	0.93[CEU][hapmap];0.97[GIH][hapmap]
rs829642	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs829646	0.86[CEU][hapmap];0.95[GIH][hapmap]
rs829653	1.00[CEU][hapmap]
rs829654	0.93[CEU][hapmap]
rs829655	0.85[CEU][hapmap]
rs829659	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs829660	0.87[EUR][1000 genomes]
rs829661	0.86[CEU][hapmap]
rs829664	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs829669	0.93[CEU][hapmap]
rs829671	0.86[CEU][hapmap]
rs829672	0.86[CEU][hapmap]
rs829673	0.85[CEU][hapmap]
rs829675	0.86[CEU][hapmap]
rs829677	0.93[CEU][hapmap]
rs829679	0.93[CEU][hapmap]
rs829680	0.86[CEU][hapmap]
rs829681	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs829682	0.91[CEU][hapmap]
rs829684	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs844194	0.93[CEU][hapmap]
rs860487	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs866680	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs895662	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895665	0.95[EUR][1000 genomes];0.83[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2609955	TMEM214	cis	cerebellum	SCAN
rs2609955	LYCAT	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 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	chr2:30860400-30878200	Weak transcription	NHLF	lung
7	chr2:30861400-30876800	Weak transcription	Fetal Heart	heart
8	chr2:30861600-30872200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:30863600-30882200	Weak transcription	Ovary	ovary
10	chr2:30864000-30874800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:30864200-30872200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:30864800-30875200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:30864800-30876600	Weak transcription	Osteobl	bone
14	chr2:30865000-30872200	Weak transcription	Aorta	Aorta
15	chr2:30865000-30875200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:30865200-30872200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:30865200-30873000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:30865200-30877000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:30865200-30878200	Weak transcription	A549	lung
20	chr2:30866800-30872200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:30869200-30878000	Weak transcription	Psoas Muscle	Psoas
22	chr2:30871400-30873600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:30871600-30872400	Enhancers	Lung	lung
24	chr2:30871600-30873000	Enhancers	Fetal Muscle Leg	muscle
25	chr2:30871800-30872200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr2:30871800-30872400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:30871800-30872400	Enhancers	Left Ventricle	heart
28	chr2:30871800-30872400	Enhancers	Stomach Smooth Muscle	stomach
29	chr2:30871800-30872600	Enhancers	HSMMtube	muscle
30	chr2:30872000-30872200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:30872000-30872200	Enhancers	Fetal Intestine Small	intestine
32	chr2:30872000-30872200	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:30872000-30872400	Enhancers	Fetal Stomach	stomach
34	chr2:30872000-30872600	Enhancers	Right Ventricle	heart
35	chr2:30872000-30872600	Enhancers	NHDF-Ad	bronchial

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