Variant report

Variant	rs1010239
Chromosome Location	chr2:86451502-86451503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86422108..86424047-chr2:86449364..86452333,2	MCF-7	breast:
2	chr2:86425356..86427237-chr2:86450431..86453375,2	K562	blood:
3	chr2:86450859..86453115-chr2:86460291..86462140,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273080	Chromatin interaction
ENSG00000132313	Chromatin interaction
ENSG00000132305	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1007502	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11944	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13000103	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs1559511	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1559514	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17438451	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2003931	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2042502	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2059352	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2241432	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2288122	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087642	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770059	0.82[CEU][hapmap]
rs4832029	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs708600	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs965636	0.81[CEU][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1010239	MRPL35	cis	lesional skin	skin_eQTL
rs1010239	IMMT	cis	Whole Blood	GTEx
rs1010239	MRPL35	cis	uninvolved skin	skin_eQTL
rs1010239	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs1010239	MRPL35	cis	normal skin	skin_eQTL
rs1010239	IMMT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86438600-86452200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:86439800-86452200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:86439800-86452200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:86440000-86452200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:86440000-86452800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:86441600-86452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:86441600-86452600	Weak transcription	Thymus	Thymus
8	chr2:86441600-86452800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:86441800-86452200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:86441800-86452400	Weak transcription	Fetal Thymus	thymus
11	chr2:86442000-86452000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:86442000-86452200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:86442400-86452000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:86442400-86452200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:86442800-86451800	Weak transcription	Primary B cells from cord blood	blood
16	chr2:86446000-86452800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:86447600-86453600	Weak transcription	Fetal Brain Female	brain
18	chr2:86448200-86452400	Enhancers	Brain Angular Gyrus	brain
19	chr2:86448200-86453200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:86448200-86454600	Enhancers	Fetal Muscle Leg	muscle
21	chr2:86448200-86454600	Enhancers	Left Ventricle	heart
22	chr2:86448400-86451800	Enhancers	Ovary	ovary
23	chr2:86448400-86452000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:86448400-86453200	Enhancers	Fetal Muscle Trunk	muscle
25	chr2:86448400-86453200	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:86448600-86452200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:86448600-86452400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:86448600-86453200	Enhancers	Fetal Stomach	stomach
29	chr2:86448600-86453400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:86448600-86453400	Enhancers	Right Atrium	heart
31	chr2:86448800-86451800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:86448800-86452000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:86449000-86451800	Weak transcription	Lung	lung
34	chr2:86449000-86452000	Weak transcription	HUVEC	blood vessel
35	chr2:86449000-86453800	Enhancers	Right Ventricle	heart
36	chr2:86449000-86454200	Enhancers	Fetal Heart	heart
37	chr2:86449400-86453000	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:86449400-86453400	Enhancers	Brain Hippocampus Middle	brain
39	chr2:86449600-86451600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr2:86449600-86453200	Enhancers	NHDF-Ad	bronchial
41	chr2:86449800-86451600	Enhancers	Fetal Intestine Small	intestine
42	chr2:86449800-86452400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:86450000-86451600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr2:86450000-86451600	Enhancers	NHEK	skin
45	chr2:86450000-86451800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:86450000-86452000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:86450000-86452000	Enhancers	HSMMtube	muscle
48	chr2:86450000-86452600	Enhancers	Adipose Nuclei	Adipose
49	chr2:86450000-86452800	Enhancers	GM12878-XiMat	blood
50	chr2:86450000-86453800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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