Variant report

Variant	rs2059353
Chromosome Location	chr2:86344367-86344368
allele	A/G
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	RFX5	chr2:86344253-86344444	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86332476..86335338-chr2:86344078..86345982,2	MCF-7	breast:
2	chr2:86344358..86346685-chr2:86348908..86351483,2	K562	blood:
3	chr2:86341666..86344435-chr2:86359867..86362807,2	MCF-7	breast:
4	chr2:86332602..86334815-chr2:86344109..86346684,2	K562	blood:

Variant related genes	Relation type
PTCD3	TF binding region
ENSG00000132300	Chromatin interaction
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10187875	1.00[ASN][1000 genomes]
rs10427394	0.87[CEU][hapmap]
rs10779967	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127015	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127018	0.88[MEX][hapmap]
rs11885520	0.92[ASN][1000 genomes]
rs11886175	1.00[ASN][1000 genomes]
rs11890563	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11891096	1.00[ASN][1000 genomes]
rs11895453	1.00[ASN][1000 genomes]
rs12473739	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs13353	0.91[ASN][1000 genomes]
rs13390107	1.00[ASN][1000 genomes]
rs13420958	1.00[ASN][1000 genomes]
rs13431245	0.92[ASN][1000 genomes]
rs1424516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424520	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs1469982	1.00[ASN][1000 genomes]
rs1559513	1.00[JPT][hapmap]
rs1559516	0.87[CEU][hapmap]
rs2288117	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2288121	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs311561	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs311567	0.83[GIH][hapmap]
rs311570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs311580	1.00[ASN][1000 genomes]
rs311581	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs311582	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs311583	1.00[ASN][1000 genomes]
rs311584	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34892520	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3770073	0.84[ASN][1000 genomes]
rs3810828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832027	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4832028	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4832239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832242	0.87[CEU][hapmap]
rs4832250	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs4832254	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs4832258	1.00[JPT][hapmap]
rs57339071	1.00[ASN][1000 genomes]
rs58077381	1.00[ASN][1000 genomes]
rs6547666	1.00[JPT][hapmap]
rs6707736	0.84[ASN][1000 genomes]
rs6715623	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723248	1.00[ASN][1000 genomes]
rs6749218	1.00[ASN][1000 genomes]
rs6752561	1.00[ASN][1000 genomes]
rs6758535	1.00[JPT][hapmap]
rs72847843	1.00[ASN][1000 genomes]
rs72847853	1.00[ASN][1000 genomes]
rs7340327	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7419344	1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs7558040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565645	1.00[JPT][hapmap]
rs7583021	0.82[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs7592211	0.91[ASN][1000 genomes]
rs7597608	0.82[ASN][1000 genomes]
rs7599498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[ASN][1000 genomes]
rs889911	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs918856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929916	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9677675	1.00[ASN][1000 genomes]
rs9679308	1.00[ASN][1000 genomes]
rs979940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2059353	POLR1A	cis	Nerve Tibial	GTEx
rs2059353	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs2059353	MRPL35	cis	Esophagus Muscularis	GTEx
rs2059353	POLR1A	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86334400-86362800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:86334800-86344400	Weak transcription	Stomach Mucosa	stomach
3	chr2:86335000-86379000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr2:86335000-86409000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:86335200-86366600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:86335200-86380800	Strong transcription	Fetal Thymus	thymus
7	chr2:86335400-86346000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:86335400-86394000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:86335400-86408800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:86335600-86366600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:86335600-86366800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:86335600-86368000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:86335600-86369200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:86335600-86373600	Strong transcription	K562	blood
15	chr2:86335600-86378800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:86335600-86379000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:86335600-86379000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:86335600-86379000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:86335600-86394000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:86335600-86401000	Strong transcription	Placenta	Placenta
21	chr2:86335600-86407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:86335600-86408600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:86335800-86356400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:86335800-86378600	Strong transcription	Fetal Brain Female	brain
25	chr2:86336000-86355600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:86336000-86365800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:86336000-86378600	Strong transcription	Brain Germinal Matrix	brain
28	chr2:86336000-86378800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:86336000-86378800	Strong transcription	Liver	Liver
30	chr2:86336000-86380800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:86336000-86401200	Strong transcription	Adipose Nuclei	Adipose
32	chr2:86336200-86366600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:86336600-86353200	Strong transcription	Primary B cells from cord blood	blood
34	chr2:86336600-86363000	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr2:86336600-86369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:86336600-86378600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:86336600-86378600	Strong transcription	Fetal Muscle Leg	muscle
38	chr2:86336600-86378800	Strong transcription	Fetal Intestine Large	intestine
39	chr2:86336600-86378800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:86336600-86378800	Strong transcription	Rectal Smooth Muscle	rectum
41	chr2:86336600-86394200	Strong transcription	Primary T cells from cord blood	blood
42	chr2:86336800-86344600	Weak transcription	Psoas Muscle	Psoas
43	chr2:86336800-86379200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:86336800-86407400	Strong transcription	Dnd41	blood
45	chr2:86337000-86345200	Strong transcription	HepG2	liver
46	chr2:86337600-86358800	Strong transcription	Fetal Stomach	stomach
47	chr2:86337600-86362400	Strong transcription	Brain Cingulate Gyrus	brain
48	chr2:86337600-86365800	Strong transcription	Thymus	Thymus
49	chr2:86337600-86367800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:86337600-86369400	Strong transcription	Spleen	Spleen

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