Variant report

Variant	rs2042502
Chromosome Location	chr2:86459249-86459250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86452854..86455973-chr2:86457257..86460636,3	K562	blood:
2	chr2:86456523..86459798-chr2:86460468..86465840,5	K562	blood:
3	chr2:86457220..86459478-chr2:86473553..86476123,2	MCF-7	breast:
4	chr2:86451560..86455569-chr2:86456212..86459487,3	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1007502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1010239	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10165626	0.90[JPT][hapmap]
rs10186289	0.95[JPT][hapmap]
rs10204589	0.90[JPT][hapmap]
rs11127016	1.00[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs11127019	0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11127024	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11676515	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11680025	0.90[JPT][hapmap]
rs11687392	0.90[JPT][hapmap]
rs11689971	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11944	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12988844	0.84[MKK][hapmap]
rs13000103	0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs13005014	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs13024436	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs1559511	0.84[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1559514	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17438451	0.82[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs17438687	0.84[MKK][hapmap]
rs17584697	1.00[YRI][hapmap]
rs17618119	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs17738058	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1863050	0.85[JPT][hapmap];1.00[MKK][hapmap]
rs1863056	0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1863057	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1863058	0.90[JPT][hapmap]
rs1863060	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1863061	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1863063	0.95[JPT][hapmap]
rs2003931	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059352	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2113615	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2194486	1.00[YRI][hapmap]
rs2241432	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2276625	0.90[JPT][hapmap]
rs2288122	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2303338	1.00[YRI][hapmap]
rs2367232	0.90[JPT][hapmap]
rs3087642	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs311578	1.00[YRI][hapmap]
rs311579	0.80[MEX][hapmap];0.86[MKK][hapmap]
rs35408390	0.82[ASN][1000 genomes]
rs3731818	1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs3764949	1.00[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs3764950	1.00[YRI][hapmap]
rs4610056	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4832029	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4832031	0.84[MKK][hapmap]
rs4832036	0.90[JPT][hapmap]
rs4832263	0.90[JPT][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs4832265	0.90[JPT][hapmap]
rs4832271	0.90[JPT][hapmap]
rs4832272	1.00[YRI][hapmap]
rs4832274	0.90[JPT][hapmap]
rs4832276	0.90[JPT][hapmap]
rs6547673	0.95[JPT][hapmap]
rs6731358	1.00[YRI][hapmap]
rs6758173	0.94[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs708600	0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes]
rs718292	0.90[JPT][hapmap];1.00[MKK][hapmap]
rs7563887	0.95[JPT][hapmap]
rs7569654	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs766285	0.81[MKK][hapmap]
rs9309635	0.90[JPT][hapmap]
rs965636	1.00[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2042502	POLR1A	cis	cerebellum	SCAN
rs2042502	VAMP5	cis	parietal	SCAN
rs2042502	SH2D6	cis	cerebellum	SCAN
rs2042502	IMMT	cis	lymphoblastoid	seeQTL
rs2042502	SFTPB	cis	cerebellum	SCAN
rs2042502	MRPL35	cis	normal skin	skin_eQTL
rs2042502	MRPL35	cis	parietal	SCAN
rs2042502	MRPL35	cis	uninvolved skin	skin_eQTL
rs2042502	REEP1	cis	parietal	SCAN
rs2042502	MRPL35	cis	cerebellum	SCAN
rs2042502	IMMT	cis	cerebellum	SCAN
rs2042502	ST3GAL5	cis	cerebellum	SCAN
rs2042502	IMMT	cis	Whole Blood	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86450800-86463400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:86450800-86476400	Weak transcription	Fetal Brain Male	brain
3	chr2:86451800-86459600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:86451800-86462400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:86452000-86462200	Weak transcription	HSMMtube	muscle
6	chr2:86452200-86461800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:86452400-86467400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:86452400-86477400	Weak transcription	Brain Angular Gyrus	brain
9	chr2:86453000-86461600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:86453000-86461600	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:86453200-86462200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:86453200-86467600	Weak transcription	Spleen	Spleen
13	chr2:86453200-86468400	Weak transcription	Gastric	stomach
14	chr2:86453200-86475800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:86453400-86461800	Weak transcription	Right Atrium	heart
16	chr2:86453400-86470400	Weak transcription	Aorta	Aorta
17	chr2:86453800-86460200	Strong transcription	Brain Germinal Matrix	brain
18	chr2:86454600-86461400	Weak transcription	Left Ventricle	heart
19	chr2:86456600-86460000	Weak transcription	Brain Anterior Caudate	brain
20	chr2:86456800-86461600	Weak transcription	Fetal Heart	heart
21	chr2:86457200-86460200	Strong transcription	Fetal Intestine Small	intestine
22	chr2:86457400-86460200	Strong transcription	Fetal Brain Female	brain
23	chr2:86457400-86460800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:86457600-86460000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr2:86457600-86460200	Genic enhancers	Fetal Muscle Leg	muscle
26	chr2:86457600-86460200	Strong transcription	Fetal Stomach	stomach
27	chr2:86458000-86463800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:86458200-86459800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:86458600-86460000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:86458600-86462400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:86458800-86459600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:86458800-86460400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:86458800-86460800	Weak transcription	Fetal Lung	lung
34	chr2:86458800-86462400	Weak transcription	Right Ventricle	heart
35	chr2:86459000-86459800	Strong transcription	Fetal Intestine Large	intestine
36	chr2:86459000-86460000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:86459200-86459400	Enhancers	Fetal Muscle Trunk	muscle
38	chr2:86459200-86459800	Enhancers	Esophagus	oesophagus
39	chr2:86459200-86460800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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