Variant report

Variant	rs2287641
Chromosome Location	chr2:54342955-54342956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54196743..54198781-chr2:54341566..54344110,2	K562	blood:
2	chr2:54342236..54343923-chr2:54879380..54882162,2	MCF-7	breast:
3	chr2:54341520..54343821-chr2:54682367..54684141,3	MCF-7	breast:
4	chr2:54341216..54345253-chr2:54347980..54351307,5	MCF-7	breast:
5	chr18:12947857..12948364-chr2:54342415..54343083,2	Hela-S3	cervix:
6	chr2:54340617..54344494-chr2:54480899..54484108,3	K562	blood:
7	chr17:79849578..79850209-chr2:54342411..54343037,2	Hela-S3	cervix:
8	chr2:54341806..54344770-chr2:54784235..54787039,2	MCF-7	breast:
9	chr2:54342420..54344092-chr20:46285600..46287785,2	MCF-7	breast:
10	chr15:76603595..76604138-chr2:54342354..54343006,2	HCT-116	colon:
11	chr16:20912054..20912881-chr2:54342309..54343237,2	Hela-S3	cervix:
12	chr2:54341515..54343973-chr2:55337394..55340042,2	MCF-7	breast:
13	chr2:54341307..54344135-chr2:54557168..54559182,2	K562	blood:
14	chr2:54342079..54343052-chr5:109024930..109025777,2	Hela-S3	cervix:
15	chr19:48281526..48282040-chr2:54342571..54343371,2	NB4	blood:
16	chr2:54341443..54343043-chr2:54557751..54559883,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000102897	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000177994	Chromatin interaction
ENSG00000115306	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000141552	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000112893	Chromatin interaction
ENSG00000178980	Chromatin interaction
ENSG00000140374	Chromatin interaction
ENSG00000178021	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10173565	0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10186140	0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.87[ASN][1000 genomes]
rs10201710	0.89[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10206954	0.89[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs11125522	0.81[ASN][1000 genomes]
rs11689599	0.84[ASN][1000 genomes]
rs11884229	0.89[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs11884435	0.89[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs12615044	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617094	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12620359	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12623320	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13399590	0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs13406537	0.83[ASN][1000 genomes]
rs13417064	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13425449	0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1421618	0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1421619	0.82[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17045536	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2112126	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2112127	0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2287640	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287644	0.96[ASN][1000 genomes]
rs2287645	0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs3738854	0.89[JPT][hapmap]
rs3850348	0.90[MEX][hapmap]
rs3929001	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs55762565	0.83[ASN][1000 genomes]
rs55994902	0.81[ASN][1000 genomes]
rs56696975	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57437150	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57536238	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57940005	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57940820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57995357	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58125959	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59495263	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59749650	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59929874	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59936071	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60798176	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61434527	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545387	0.89[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs6713993	0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6742463	0.85[ASN][1000 genomes]
rs7558563	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7572559	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7574376	0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7585466	0.93[ASN][1000 genomes]
rs7593897	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs918356	0.94[ASN][1000 genomes]
rs9631060	0.85[ASN][1000 genomes]
rs977784	0.89[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1851003	chr2:54324701-54372931	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
12	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
13	nsv961690	chr2:54339295-54359290	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2287641	ACYP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54341800-54343000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:54341800-54343200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54341800-54343200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr2:54341800-54343200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:54341800-54343200	Active TSS	K562	blood
6	chr2:54341800-54343400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:54341800-54343400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:54341800-54343400	Active TSS	GM12878-XiMat	blood
9	chr2:54341800-54343600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:54341800-54343600	Active TSS	Muscle Satellite Cultured Cells	--
11	chr2:54341800-54343600	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr2:54341800-54343600	Active TSS	A549	lung
13	chr2:54341800-54344000	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr2:54342000-54343200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr2:54342000-54343200	Active TSS	Fetal Brain Female	brain
16	chr2:54342000-54343400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr2:54342000-54343400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr2:54342000-54343400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr2:54342000-54343400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr2:54342000-54343400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:54342000-54343400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:54342000-54343400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:54342000-54343400	Active TSS	Left Ventricle	heart
24	chr2:54342000-54343400	Active TSS	HSMM	muscle
25	chr2:54342000-54343400	Active TSS	NHDF-Ad	bronchial
26	chr2:54342000-54343600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr2:54342000-54343600	Active TSS	NHLF	lung
28	chr2:54342200-54343200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:54342200-54343200	Active TSS	Dnd41	blood
30	chr2:54342200-54343400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:54342200-54343400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:54342200-54343400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:54342200-54343400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:54342200-54343400	Active TSS	Aorta	Aorta
35	chr2:54342200-54343400	Active TSS	Colonic Mucosa	Colon
36	chr2:54342200-54343400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr2:54342200-54343400	Active TSS	Fetal Muscle Trunk	muscle
38	chr2:54342200-54343400	Active TSS	Fetal Stomach	stomach
39	chr2:54342200-54343400	Active TSS	Fetal Thymus	thymus
40	chr2:54342200-54343400	Active TSS	Psoas Muscle	Psoas
41	chr2:54342200-54343400	Active TSS	Right Ventricle	heart
42	chr2:54342200-54343400	Active TSS	Thymus	Thymus
43	chr2:54342200-54343400	Active TSS	HSMMtube	muscle
44	chr2:54342200-54343600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:54342200-54343600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:54342200-54343600	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr2:54342200-54343600	Active TSS	Brain Cingulate Gyrus	brain
48	chr2:54342200-54343600	Active TSS	Brain Germinal Matrix	brain
49	chr2:54342200-54343600	Active TSS	Brain Hippocampus Middle	brain
50	chr2:54342200-54343600	Active TSS	Fetal Muscle Leg	muscle

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