Variant report

Variant	rs62260771
Chromosome Location	chr3:50165563-50165564
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50160600..50163125-chr3:50165110..50166972,2	K562	blood:
2	chr3:50164743..50166299-chr3:50183403..50185616,2	MCF-7	breast:
3	chr3:50157879..50160528-chr3:50162974..50166130,4	K562	blood:
4	chr3:50164220..50165841-chr3:50169417..50171104,2	MCF-7	breast:
5	chr3:50157840..50167526-chr3:50182100..50196634,43	MCF-7	breast:
6	chr3:50164983..50167115-chr3:50208238..50210374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235016	Chromatin interaction
ENSG00000001617	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11130237	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11130240	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11916999	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920034	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924670	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924711	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928995	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486470	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486808	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12490944	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12492291	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494077	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494172	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494916	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495114	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629129	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12629677	0.89[AMR][1000 genomes]
rs12631248	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631306	0.89[AMR][1000 genomes]
rs12631309	0.89[AMR][1000 genomes]
rs12632751	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636045	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636449	0.90[EUR][1000 genomes]
rs12636669	0.89[AMR][1000 genomes]
rs12637222	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12637457	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12638046	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13100903	0.94[ASN][1000 genomes]
rs2003485	0.87[ASN][1000 genomes]
rs2023951	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023952	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35333166	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57009357	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs59802870	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60429865	0.84[EUR][1000 genomes]
rs61491513	0.89[AMR][1000 genomes]
rs61729114	0.89[AMR][1000 genomes]
rs62260770	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260773	0.86[EUR][1000 genomes]
rs62262096	0.89[AMR][1000 genomes]
rs62262099	0.89[AMR][1000 genomes]
rs62262104	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262116	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262138	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262144	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62263578	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62263580	0.81[EUR][1000 genomes]
rs62263584	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263586	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263588	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263590	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263591	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263596	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263597	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62263600	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv818139	chr3:50144951-50174572	Weak transcription Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
8	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
11	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
12	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
13	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
14	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
15	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
16	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50151000-50176400	Weak transcription	Right Atrium	heart
2	chr3:50159800-50168600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:50161800-50165800	Enhancers	Brain Germinal Matrix	brain
4	chr3:50163200-50165600	Enhancers	Duodenum Mucosa	Duodenum
5	chr3:50163600-50165800	Enhancers	Fetal Kidney	kidney
6	chr3:50163600-50166200	Enhancers	Gastric	stomach
7	chr3:50164000-50170800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:50164200-50165600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:50164200-50166000	Enhancers	HepG2	liver
10	chr3:50164200-50170000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:50164400-50169800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:50164400-50174600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:50164600-50172600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:50164600-50174200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:50164800-50165600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:50164800-50167800	Weak transcription	Spleen	Spleen
17	chr3:50164800-50170200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:50165000-50167800	Weak transcription	Fetal Stomach	stomach
19	chr3:50165000-50168000	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:50165000-50170000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:50165000-50170000	Weak transcription	Fetal Brain Male	brain
22	chr3:50165000-50170000	Weak transcription	Fetal Brain Female	brain
23	chr3:50165200-50165600	Weak transcription	Stomach Mucosa	stomach
24	chr3:50165200-50165800	Weak transcription	Lung	lung
25	chr3:50165200-50169800	Weak transcription	Stomach Smooth Muscle	stomach

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