Variant report

Variant	rs1058320
Chromosome Location	chr2:54312153-54312154
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:54311629-54312617	A549	lung:	n/a	n/a
2	RAD21	chr2:54311748-54312256	HCT-116	colon:	n/a	n/a
3	RAD21	chr2:54311622-54312524	HepG2	liver:	n/a	n/a
4	RAD21	chr2:54311745-54312519	A549	lung:	n/a	n/a
5	RAD21	chr2:54311677-54312234	MCF-7	breast:	n/a	n/a
6	CTCF	chr2:54311710-54312592	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr2:54311702-54312654	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr2:54311779-54312174	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54304842..54306570-chr2:54310702..54313482,3	K562	blood:
2	chr2:54310362..54312411-chr2:54340421..54343349,2	MCF-7	breast:
3	chr2:54279392..54279928-chr2:54311498..54312280,2	MCF-7	breast:
4	chr2:54310601..54313895-chr2:54315141..54317483,3	MCF-7	breast:
5	chr2:54279730..54280237-chr2:54311516..54312403,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSME4-2	chr2:54311715-54312205	NONHSAT070719
2	lnc-ACYP2-2	chr2:54311707-54312203	ENSG00000272156.1

No data

Variant related genes	Relation type
ENSG00000241114	TF binding region
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10084355	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10201364	0.81[AMR][1000 genomes]
rs10203576	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10207537	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208233	0.86[EUR][1000 genomes]
rs1075265	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865277	0.80[ASN][1000 genomes]
rs10865279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11125519	0.81[AMR][1000 genomes]
rs11125520	0.80[ASN][1000 genomes]
rs11125524	0.84[ASN][1000 genomes]
rs1118618	0.93[EUR][1000 genomes]
rs11687324	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11695734	0.98[ASN][1000 genomes]
rs11887549	0.81[ASN][1000 genomes]
rs11888384	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11896781	0.87[ASN][1000 genomes]
rs1215150	0.89[CHB][hapmap]
rs12616638	0.85[ASN][1000 genomes]
rs12713253	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13418779	0.82[AMR][1000 genomes]
rs1363062	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1363063	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1421617	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1421622	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17268179	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1727522	0.87[CHB][hapmap]
rs1833497	0.91[ASN][1000 genomes]
rs1833498	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1862121	0.93[ASN][1000 genomes]
rs1862122	0.91[ASN][1000 genomes]
rs1877906	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2018747	0.98[ASN][1000 genomes]
rs2042143	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2048749	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2111868	0.83[CEU][hapmap]
rs2112124	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2287642	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2357954	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2884254	0.80[AMR][1000 genomes]
rs34769118	0.85[ASN][1000 genomes]
rs41385746	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs4671178	0.93[ASN][1000 genomes]
rs4671190	0.99[ASN][1000 genomes]
rs4671860	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671872	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56001939	0.81[ASN][1000 genomes]
rs62137965	0.89[ASN][1000 genomes]
rs6545378	0.80[AMR][1000 genomes]
rs6545384	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545388	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545389	0.85[CEU][hapmap]
rs6724389	0.85[CEU][hapmap]
rs6741891	0.99[ASN][1000 genomes]
rs6749817	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs718872	0.84[CEU][hapmap]
rs7558126	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7560947	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562055	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7566894	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7569214	0.92[CEU][hapmap]
rs7569370	0.92[CEU][hapmap]
rs7569743	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7571086	0.81[AMR][1000 genomes]
rs7573491	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7574477	0.87[CHB][hapmap]
rs7591194	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604357	0.98[ASN][1000 genomes]
rs7607066	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs805308	0.89[CEU][hapmap]
rs805309	0.92[CEU][hapmap]
rs805322	0.81[CEU][hapmap]
rs805341	0.88[CEU][hapmap]
rs805367	0.81[CEU][hapmap]
rs805450	0.85[CEU][hapmap]
rs843675	0.81[CHB][hapmap]
rs843677	0.87[CHB][hapmap]
rs888635	0.98[ASN][1000 genomes]
rs918357	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs929734	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs959286	0.89[CHB][hapmap]
rs9808326	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1058320	ACYP2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
2	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
4	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
5	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:54294800-54315000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:54295200-54312200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:54302800-54317800	Weak transcription	Left Ventricle	heart
9	chr2:54305000-54315000	Weak transcription	Fetal Intestine Large	intestine
10	chr2:54305000-54315200	Weak transcription	Pancreas	Pancrea
11	chr2:54305400-54321600	Weak transcription	Lung	lung
12	chr2:54306600-54315400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:54307400-54319400	Weak transcription	Primary T cells from cord blood	blood
14	chr2:54309000-54315200	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:54309000-54317600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:54309200-54315400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:54309200-54315600	Weak transcription	Esophagus	oesophagus
18	chr2:54309400-54315000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:54309400-54315000	Weak transcription	NHEK	skin
20	chr2:54309400-54315200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:54309800-54315000	Weak transcription	HMEC	breast
22	chr2:54310800-54313400	Weak transcription	K562	blood
23	chr2:54310800-54315200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:54310800-54315200	Weak transcription	NH-A	brain
25	chr2:54311000-54313800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:54311000-54314600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:54311000-54315000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:54311000-54315200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:54311000-54315200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:54311000-54315200	Weak transcription	Right Atrium	heart
31	chr2:54311000-54317800	Weak transcription	Brain Anterior Caudate	brain
32	chr2:54311000-54317800	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:54311000-54324200	Weak transcription	HSMMtube	muscle
34	chr2:54311600-54312200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:54311800-54317600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:54312000-54315200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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