Variant report

Variant	rs805309
Chromosome Location	chr2:54196014-54196015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54195426-54199062	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr2:54195947-54196076	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:54195526-54196830	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:54195490-54199155	PBDE	blood:	n/a	n/a
5	FOXA2	chr2:54195632-54197176	HepG2	liver:	n/a	n/a
6	CHD1	chr2:54195365-54199244	IMR90	lung:	n/a	n/a
7	JUN	chr2:54195869-54197641	K562	blood:	n/a	chr2:54196588-54196596 chr2:54196588-54196596 chr2:54196584-54196595 chr2:54196589-54196596 chr2:54196587-54196597
8	MXI1	chr2:54195676-54199239	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54165576..54167252-chr2:54193257..54196468,3	K562	blood:
2	chr2:54195012..54197478-chr2:54219368..54222229,2	K562	blood:
3	chr2:54185625..54188123-chr2:54194333..54197670,3	MCF-7	breast:
4	chr2:54195792..54198215-chr2:55457941..55460893,2	K562	blood:
5	chr2:54184275..54188127-chr2:54193177..54197889,6	K562	blood:
6	chr2:54157567..54166967-chr2:54194910..54201681,12	MCF-7	breast:
7	chr2:54176939..54180611-chr2:54194148..54196574,3	K562	blood:
8	chr2:54195961..54197468-chr2:54240342..54242610,2	MCF-7	breast:
9	chr2:54194885..54197429-chr2:55459526..55461126,2	MCF-7	breast:
10	chr2:54194904..54197235-chr2:54307312..54309509,2	K562	blood:

Variant related genes	Relation type
ACYP2	TF binding region
ENSG00000068878	Chromatin interaction
ENSG00000241114	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10084355	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10183655	0.80[CEU][hapmap]
rs10201364	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10203576	0.85[AMR][1000 genomes]
rs1058320	0.92[CEU][hapmap]
rs1075265	0.96[CEU][hapmap]
rs11125519	0.86[AMR][1000 genomes]
rs11683654	0.86[CHB][hapmap]
rs11687324	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12616212	0.86[EUR][1000 genomes]
rs12713253	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13414393	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1363062	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1363063	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1421617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1421622	0.85[AMR][1000 genomes]
rs17045439	0.80[JPT][hapmap]
rs17268179	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2111868	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287642	0.92[CEU][hapmap]
rs2302878	0.80[JPT][hapmap]
rs2884254	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909460	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3731967	0.80[CEU][hapmap]
rs4671872	0.92[CEU][hapmap]
rs6545376	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545378	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545388	0.92[CEU][hapmap]
rs6545389	0.83[CEU][hapmap]
rs6713088	0.81[CEU][hapmap]
rs6724389	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6746965	0.81[CEU][hapmap]
rs6749817	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs698858	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs718872	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7566894	0.92[CEU][hapmap]
rs7569214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7569370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7571086	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7609017	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805308	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805322	0.88[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805335	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs805341	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805342	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs805343	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805345	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805358	0.84[AMR][1000 genomes]
rs805359	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs805360	0.85[CHB][hapmap]
rs805361	0.84[AMR][1000 genomes]
rs805366	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs805367	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs805373	0.90[JPT][hapmap]
rs805374	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs805375	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes]
rs805379	0.82[AMR][1000 genomes]
rs805380	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs805391	0.83[AMR][1000 genomes]
rs805392	0.82[AMR][1000 genomes]
rs805393	0.81[AMR][1000 genomes]
rs805402	0.85[AMR][1000 genomes]
rs805410	0.80[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs805412	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs805421	0.86[AMR][1000 genomes]
rs805422	0.80[AMR][1000 genomes]
rs805423	0.84[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes]
rs805424	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs805438	0.88[CEU][hapmap]
rs805439	0.88[CEU][hapmap]
rs805444	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs805450	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805453	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs809280	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs918357	0.91[CEU][hapmap]
rs929734	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs805309	ACYP2	cis	Muscle Skeletal	GTEx
rs805309	ACYP2	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54176200-54196200	Weak transcription	Placenta	Placenta
2	chr2:54189800-54196400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:54190000-54196400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54190400-54197000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:54190600-54196400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:54190600-54197000	Weak transcription	Esophagus	oesophagus
7	chr2:54192600-54196400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:54192600-54197000	Weak transcription	Spleen	Spleen
9	chr2:54193600-54196400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:54194000-54197000	Weak transcription	Gastric	stomach
11	chr2:54194000-54198800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr2:54194200-54196600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr2:54194400-54196200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:54194400-54196600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:54194400-54197000	Flanking Active TSS	Dnd41	blood
16	chr2:54194800-54196200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:54194800-54196200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:54194800-54196200	Flanking Active TSS	HUVEC	blood vessel
19	chr2:54194800-54198800	Active TSS	Osteobl	bone
20	chr2:54194800-54199400	Active TSS	HSMMtube	muscle
21	chr2:54195000-54196400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:54195000-54196800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:54195000-54198800	Active TSS	HMEC	breast
24	chr2:54195000-54199200	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr2:54195000-54199400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:54195200-54196200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr2:54195200-54196400	Flanking Active TSS	Liver	Liver
28	chr2:54195200-54197000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:54195200-54197400	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr2:54195200-54199200	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:54195200-54199400	Active TSS	HSMM	muscle
32	chr2:54195400-54196200	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr2:54195400-54196200	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr2:54195400-54196200	Enhancers	Brain Germinal Matrix	brain
35	chr2:54195400-54196200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:54195400-54196200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr2:54195400-54196200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr2:54195400-54196400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:54195400-54196400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:54195400-54196400	Enhancers	Fetal Intestine Large	intestine
41	chr2:54195400-54196400	Flanking Active TSS	A549	lung
42	chr2:54195400-54196600	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr2:54195400-54197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:54195400-54197000	Weak transcription	Lung	lung
45	chr2:54195400-54197000	Weak transcription	Pancreas	Pancrea
46	chr2:54195400-54197200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr2:54195400-54197400	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr2:54195400-54198000	Active TSS	Right Atrium	heart
49	chr2:54195400-54198600	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr2:54195400-54199000	Active TSS	Left Ventricle	heart

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