Variant report

Variant	rs6547659
Chromosome Location	chr2:86340613-86340614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86338856..86341007-chr2:86344850..86347667,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10165327	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10179090	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10183744	0.84[AMR][1000 genomes]
rs1019592	0.87[AMR][1000 genomes]
rs10427394	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1075622	0.84[AMR][1000 genomes]
rs10779967	0.85[CEU][hapmap]
rs11679343	0.87[AMR][1000 genomes]
rs12617717	0.87[ASN][1000 genomes]
rs12621992	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12624126	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1424516	0.85[CEU][hapmap]
rs1424517	0.84[AMR][1000 genomes]
rs1424520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559515	0.84[AMR][1000 genomes]
rs1559516	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1559517	0.84[AMR][1000 genomes]
rs1834163	0.84[AMR][1000 genomes]
rs1991106	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2018608	0.87[ASN][1000 genomes]
rs2059353	0.85[CEU][hapmap]
rs2241435	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2241436	0.84[AMR][1000 genomes]
rs2278084	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288119	0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2288121	1.00[CEU][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2303339	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2367201	0.84[AMR][1000 genomes]
rs2367202	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs311565	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs311567	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs311569	1.00[CEU][hapmap]
rs311571	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs311572	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs311573	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs311581	0.85[CEU][hapmap]
rs3731820	0.84[AMR][1000 genomes]
rs3770069	0.84[AMR][1000 genomes]
rs3810828	0.85[CEU][hapmap]
rs3815840	0.81[AMR][1000 genomes]
rs4832021	0.81[AMR][1000 genomes]
rs4832022	0.84[AMR][1000 genomes]
rs4832024	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4832239	0.85[CEU][hapmap]
rs4832242	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4832247	0.84[AMR][1000 genomes]
rs4832248	0.84[AMR][1000 genomes]
rs4832249	0.84[AMR][1000 genomes]
rs4832250	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720143	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720431	0.85[CEU][hapmap]
rs6740228	0.84[AMR][1000 genomes]
rs6741577	0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs6750581	0.84[AMR][1000 genomes]
rs7558040	0.85[CEU][hapmap]
rs7606421	0.84[AMR][1000 genomes]
rs918856	0.85[CEU][hapmap]
rs979940	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
rs6547659	POLR1A	cis	Esophagus Muscularis	GTEx
rs6547659	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs6547659	POLR1A	cis	Nerve Tibial	GTEx
rs6547659	MRPL35	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86334200-86342000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86334400-86342000	Weak transcription	Pancreas	Pancrea
3	chr2:86334400-86362800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:86334800-86341400	Weak transcription	Small Intestine	intestine
5	chr2:86334800-86344400	Weak transcription	Stomach Mucosa	stomach
6	chr2:86335000-86342400	Weak transcription	Fetal Kidney	kidney
7	chr2:86335000-86379000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:86335000-86409000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:86335200-86342200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:86335200-86344200	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:86335200-86366600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr2:86335200-86380800	Strong transcription	Fetal Thymus	thymus
13	chr2:86335400-86341000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:86335400-86342000	Weak transcription	Brain Substantia Nigra	brain
15	chr2:86335400-86346000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:86335400-86394000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:86335400-86408800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:86335600-86341000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:86335600-86341000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:86335600-86341000	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr2:86335600-86366600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:86335600-86366800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:86335600-86368000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:86335600-86369200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:86335600-86373600	Strong transcription	K562	blood
26	chr2:86335600-86378800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:86335600-86379000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:86335600-86379000	Strong transcription	Duodenum Mucosa	Duodenum
29	chr2:86335600-86379000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr2:86335600-86394000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:86335600-86401000	Strong transcription	Placenta	Placenta
32	chr2:86335600-86407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:86335600-86408600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:86335800-86356400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr2:86335800-86378600	Strong transcription	Fetal Brain Female	brain
36	chr2:86336000-86355600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:86336000-86365800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:86336000-86378600	Strong transcription	Brain Germinal Matrix	brain
39	chr2:86336000-86378800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:86336000-86378800	Strong transcription	Liver	Liver
41	chr2:86336000-86380800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:86336000-86401200	Strong transcription	Adipose Nuclei	Adipose
43	chr2:86336200-86366600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:86336600-86353200	Strong transcription	Primary B cells from cord blood	blood
45	chr2:86336600-86363000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr2:86336600-86369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:86336600-86378600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:86336600-86378600	Strong transcription	Fetal Muscle Leg	muscle
49	chr2:86336600-86378800	Strong transcription	Fetal Intestine Large	intestine
50	chr2:86336600-86378800	Strong transcription	Fetal Muscle Trunk	muscle

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