Variant report

Variant	rs4671861
Chromosome Location	chr2:54341867-54341868
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:8)
LncRNA
region (count:0)
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	POLR2A	chr2:54341847-54343410	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:54341621-54343455	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:54341803-54343446	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:54341704-54343391	HepG2	liver:	n/a	n/a
5	HEY1	chr2:54341822-54343409	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:54341713-54342071	GM12878	blood:	n/a	n/a
7	MYBL2	chr2:54341649-54343366	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:54341866-54343216	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:54196743..54198781-chr2:54341566..54344110,2	K562	blood:
2	chr2:54341520..54343821-chr2:54682367..54684141,3	MCF-7	breast:
3	chr2:54341216..54345253-chr2:54347980..54351307,5	MCF-7	breast:
4	chr2:54340617..54344494-chr2:54480899..54484108,3	K562	blood:
5	chr2:54341806..54344770-chr2:54784235..54787039,2	MCF-7	breast:
6	chr2:54341515..54343973-chr2:55337394..55340042,2	MCF-7	breast:
7	chr2:54341307..54344135-chr2:54557168..54559182,2	K562	blood:
8	chr2:54341443..54343043-chr2:54557751..54559883,2	MCF-7	breast:

No data

Variant related genes	Relation type
ACYP2	TF binding region
ENSG00000115306	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000177994	Chromatin interaction
ENSG00000178021	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10496028	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1075264	0.93[ASN][1000 genomes]
rs11676462	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11896815	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11898855	0.82[AMR][1000 genomes]
rs17039547	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17045474	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17045488	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1877907	0.89[ASN][1000 genomes]
rs1877908	0.88[ASN][1000 genomes]
rs2287639	0.91[ASN][1000 genomes]
rs2287643	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357896	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34498089	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34773403	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55649409	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55705819	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56193146	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62137964	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62137976	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62137980	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62140990	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62141002	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545381	0.80[AMR][1000 genomes]
rs6545386	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6706363	0.90[ASN][1000 genomes]
rs6713088	0.96[ASN][1000 genomes]
rs6714450	0.82[AMR][1000 genomes]
rs6721970	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6751105	0.90[ASN][1000 genomes]
rs7559380	0.90[ASN][1000 genomes]
rs7559384	0.80[AMR][1000 genomes]
rs7565453	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7573551	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7576901	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7590819	0.87[AMR][1000 genomes];0.85[EUR][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
rs4671861	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:54331200-54342000	Weak transcription	Psoas Muscle	Psoas
3	chr2:54331200-54342400	Weak transcription	Pancreas	Pancrea
4	chr2:54331400-54342200	Weak transcription	Aorta	Aorta
5	chr2:54334800-54342000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:54335800-54342000	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:54336000-54342000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:54336000-54342000	Weak transcription	NHEK	skin
9	chr2:54341200-54342200	Flanking Active TSS	Dnd41	blood
10	chr2:54341400-54342000	Enhancers	HepG2	liver
11	chr2:54341600-54342000	Enhancers	Liver	Liver
12	chr2:54341600-54342000	Enhancers	Fetal Thymus	thymus
13	chr2:54341600-54342000	Active TSS	Rectal Smooth Muscle	rectum
14	chr2:54341600-54342000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr2:54341600-54342200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:54341600-54342200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:54341600-54342200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:54341600-54342400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:54341800-54342000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr2:54341800-54342000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr2:54341800-54342000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:54341800-54342000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:54341800-54342000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:54341800-54342000	Enhancers	Primary B cells from cord blood	blood
25	chr2:54341800-54342000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr2:54341800-54342000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:54341800-54342000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:54341800-54342000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:54341800-54342000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr2:54341800-54342000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:54341800-54342000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr2:54341800-54342000	Enhancers	Brain Germinal Matrix	brain
33	chr2:54341800-54342000	Enhancers	Colon Smooth Muscle	Colon
34	chr2:54341800-54342000	Enhancers	Duodenum Mucosa	Duodenum
35	chr2:54341800-54342000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr2:54341800-54342000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr2:54341800-54342000	Active TSS	Fetal Kidney	kidney
38	chr2:54341800-54342000	Enhancers	Hela-S3	cervix
39	chr2:54341800-54342000	Enhancers	HSMM	muscle
40	chr2:54341800-54342000	Enhancers	HUVEC	blood vessel
41	chr2:54341800-54342000	Enhancers	Osteobl	bone
42	chr2:54341800-54342200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:54341800-54342200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:54341800-54342200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:54341800-54342200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:54341800-54342200	Enhancers	Primary B cells from peripheral blood	blood
47	chr2:54341800-54342200	Enhancers	Primary T cells from cord blood	blood
48	chr2:54341800-54342200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr2:54341800-54342200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr2:54341800-54342200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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