Variant report

Variant	rs6725046
Chromosome Location	chr2:86424249-86424250
allele	A/C
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	chr2:86423769-86424450	K562	blood:	n/a	n/a
2	POLR2A	chr2:86424168-86424529	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86329731..86334667-chr2:86420655..86424478,8	K562	blood:
2	chr2:86398317..86400086-chr2:86422606..86424592,2	MCF-7	breast:
3	chr2:86420213..86424453-chr2:86424933..86430971,16	MCF-7	breast:

Variant related genes	Relation type
MRPL35	TF binding region
MIR4779	TF binding region
IMMT	TF binding region
ENSG00000132313	Chromatin interaction
ENSG00000132300	Chromatin interaction
ENSG00000132305	Chromatin interaction
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10173155	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10175330	0.83[GIH][hapmap]
rs10184462	0.83[CEU][hapmap]
rs10195199	0.85[CEU][hapmap]
rs10201457	0.86[MEX][hapmap]
rs1057893	0.83[GIH][hapmap]
rs10779967	0.83[ASW][hapmap]
rs11127016	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap]
rs11900161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12714175	0.85[CEU][hapmap]
rs12714177	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs12996308	0.83[GIH][hapmap]
rs13000103	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs13001470	0.81[CEU][hapmap]
rs13007807	0.81[CEU][hapmap]
rs13027248	0.85[CEU][hapmap]
rs13403186	0.89[CEU][hapmap]
rs17551822	0.80[EUR][1000 genomes]
rs17584697	0.86[CHB][hapmap]
rs2059352	0.87[ASN][1000 genomes]
rs2194486	0.86[CHB][hapmap]
rs2241432	0.84[CHB][hapmap]
rs2288113	0.83[GIH][hapmap]
rs2288122	0.87[CHB][hapmap]
rs2303338	0.86[CHB][hapmap]
rs2367203	0.83[GIH][hapmap]
rs311576	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs311578	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs311579	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs3731818	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs3764949	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap]
rs3764950	0.81[CHB][hapmap]
rs3821017	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs4374375	0.83[GIH][hapmap]
rs4402761	0.83[GIH][hapmap]
rs4422155	0.83[GIH][hapmap]
rs4450596	0.83[GIH][hapmap]
rs4544439	0.83[GIH][hapmap]
rs4832027	0.83[ASW][hapmap]
rs4832233	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs6547665	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs6707029	0.80[CEU][hapmap]
rs6729732	0.83[GIH][hapmap]
rs6731358	0.86[CHB][hapmap]
rs6731995	0.83[GIH][hapmap]
rs6735014	0.81[CEU][hapmap]
rs6740044	0.81[CEU][hapmap]
rs6749090	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs6758173	0.82[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs717144	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7422930	0.85[CEU][hapmap]
rs7560376	0.85[CEU][hapmap]
rs7563742	0.85[CEU][hapmap]
rs7567380	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7572386	0.81[CEU][hapmap]
rs7590445	0.88[CEU][hapmap]
rs7609008	0.83[GIH][hapmap]
rs9309633	0.81[CEU][hapmap]
rs9653508	0.89[CEU][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes]
rs965636	0.86[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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
19	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv458574	chr2:86385728-86507688	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
21	nsv582372	chr2:86385728-86507688	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6725046	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs6725046	MRPL35	cis	uninvolved skin	skin_eQTL
rs6725046	IMMT	cis	multi-tissue	Pritchard
rs6725046	IMMT	cis	Esophagus Muscularis	GTEx
rs6725046	IMMT	cis	cerebellum	SCAN
rs6725046	IMMT	cis	Whole Blood	GTEx
rs6725046	VPS24	cis	parietal	SCAN
rs6725046	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs6725046	IMMT	cis	lymphoblastoid	seeQTL
rs6725046	MRPL35	cis	parietal	SCAN
rs6725046	REEP1	cis	parietal	SCAN
rs6725046	MRPL35	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86423000-86424400	Flanking Active TSS	Dnd41	blood
2	chr2:86423200-86425800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:86423200-86426200	Weak transcription	Ovary	ovary
4	chr2:86423400-86424400	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr2:86423400-86424400	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr2:86423400-86424400	Enhancers	HSMMtube	muscle
7	chr2:86423400-86425400	Weak transcription	Adipose Nuclei	Adipose
8	chr2:86423400-86425600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:86423400-86425800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:86423400-86425800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:86423400-86425800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:86423400-86425800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:86423400-86425800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:86423400-86425800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:86423400-86425800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:86423400-86425800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:86423400-86425800	Weak transcription	Brain Substantia Nigra	brain
18	chr2:86423400-86425800	Weak transcription	Colonic Mucosa	Colon
19	chr2:86423400-86425800	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:86423400-86425800	Weak transcription	Placenta	Placenta
21	chr2:86423400-86425800	Weak transcription	Left Ventricle	heart
22	chr2:86423400-86425800	Weak transcription	Lung	lung
23	chr2:86423400-86425800	Weak transcription	Right Ventricle	heart
24	chr2:86423400-86425800	Weak transcription	Stomach Mucosa	stomach
25	chr2:86423400-86425800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:86423400-86425800	Weak transcription	Thymus	Thymus
27	chr2:86423400-86425800	Weak transcription	NH-A	brain
28	chr2:86423400-86426000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:86423400-86426000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:86423400-86426000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:86423400-86426000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:86423400-86426000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:86423400-86426000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:86423400-86426000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:86423400-86426000	Weak transcription	Primary T cells from cord blood	blood
36	chr2:86423400-86426000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:86423400-86426000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:86423400-86426000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:86423400-86426000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:86423400-86426000	Weak transcription	Fetal Intestine Large	intestine
41	chr2:86423400-86426000	Weak transcription	Fetal Intestine Small	intestine
42	chr2:86423400-86426000	Weak transcription	Fetal Lung	lung
43	chr2:86423400-86426000	Weak transcription	Fetal Stomach	stomach
44	chr2:86423400-86426000	Weak transcription	Pancreas	Pancrea
45	chr2:86423400-86426000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:86423400-86426000	Weak transcription	Right Atrium	heart
47	chr2:86423400-86426200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:86423400-86426200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:86423400-86426200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:86423400-86426200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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