Variant report

Variant	rs2692514
Chromosome Location	chr2:54024626-54024627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54016706..54018881-chr2:54023439..54026014,2	K562	blood:
2	chr2:53994110..53996548-chr2:54024126..54025670,2	K562	blood:

Variant related genes	Relation type
ENSG00000143942	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10183655	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs17039525	0.88[ASN][1000 genomes]
rs17045199	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.88[ASN][1000 genomes]
rs2253760	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2542571	0.94[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2542575	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542577	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542588	0.95[LWK][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs2692516	0.81[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2692534	0.81[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2909261	0.92[ASN][1000 genomes]
rs3095756	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35487539	0.89[ASN][1000 genomes]
rs3731967	0.81[CHB][hapmap]
rs3731970	0.81[ASN][1000 genomes]
rs3770407	0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs3770408	0.81[ASN][1000 genomes]
rs3770409	0.81[ASN][1000 genomes]
rs58359565	0.89[ASN][1000 genomes]
rs62137566	0.83[ASN][1000 genomes]
rs6746965	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs698853	0.93[ASN][1000 genomes]
rs698855	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap]
rs7583622	0.81[CHB][hapmap];0.97[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs766075	0.81[CHB][hapmap]
rs805321	0.86[CHB][hapmap]
rs805328	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs805351	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs805352	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs805365	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs805386	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs805399	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs805401	0.86[CHB][hapmap]
rs805404	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs805408	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs805426	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv963914	chr2:54021710-54028552	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2692514	ACYP2	cis	Esophagus Muscularis	GTEx
rs2692514	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54025400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:54015200-54029800	Weak transcription	Esophagus	oesophagus
3	chr2:54015200-54038200	Weak transcription	Small Intestine	intestine
4	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
6	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
7	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:54015600-54029600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:54015600-54035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:54015600-54035800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:54015800-54024800	Weak transcription	HUVEC	blood vessel
13	chr2:54015800-54025000	Weak transcription	Right Ventricle	heart
14	chr2:54015800-54025200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:54015800-54026000	Weak transcription	Fetal Brain Male	brain
16	chr2:54015800-54028600	Weak transcription	HMEC	breast
17	chr2:54015800-54029400	Weak transcription	Brain Substantia Nigra	brain
18	chr2:54015800-54029600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:54015800-54029800	Weak transcription	Psoas Muscle	Psoas
20	chr2:54015800-54029800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:54015800-54038400	Weak transcription	Fetal Heart	heart
22	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:54016000-54031600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:54016200-54028600	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:54016400-54025400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:54016400-54043000	Weak transcription	Gastric	stomach
27	chr2:54016800-54025000	Weak transcription	Spleen	Spleen
28	chr2:54017400-54031000	Weak transcription	Ovary	ovary
29	chr2:54017800-54027400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:54020200-54025000	Weak transcription	Pancreas	Pancrea
31	chr2:54020200-54029600	Weak transcription	Brain Angular Gyrus	brain
32	chr2:54020200-54046200	Weak transcription	Colonic Mucosa	Colon
33	chr2:54020400-54025800	Weak transcription	NHLF	lung
34	chr2:54020600-54047200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:54020600-54048400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:54020600-54048600	Strong transcription	Osteobl	bone
37	chr2:54020800-54025000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:54021000-54027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:54021000-54029200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:54021000-54030600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:54021000-54030600	Strong transcription	HepG2	liver
42	chr2:54021000-54047200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr2:54021000-54047200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:54021000-54047400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:54021000-54048000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:54021200-54030000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:54021200-54030600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:54021200-54047200	Strong transcription	Placenta	Placenta
49	chr2:54021200-54047600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:54021400-54047000	Strong transcription	Primary T helper cells PMA-I stimulated	--

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