Variant report

Variant	rs598425
Chromosome Location	chr3:105260798-105260799
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105259203..105260884-chr3:105262936..105265774,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170017	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11710166	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11710857	0.85[ASN][1000 genomes]
rs11713535	0.94[ASN][1000 genomes]
rs11714275	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11714277	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11715283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11716035	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11718405	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11718457	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11719817	0.85[ASN][1000 genomes]
rs1898655	0.88[ASN][1000 genomes]
rs1955135	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2200473	0.94[ASN][1000 genomes]
rs2399049	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895300	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs34029528	0.85[ASN][1000 genomes]
rs3772542	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772544	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772556	0.81[YRI][hapmap];0.89[AFR][1000 genomes]
rs481177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495691	0.81[EUR][1000 genomes]
rs526297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57986655	0.94[ASN][1000 genomes]
rs583889	0.85[YRI][hapmap]
rs59322590	0.88[ASN][1000 genomes]
rs61522255	0.88[ASN][1000 genomes]
rs6771935	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs6771987	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs6786815	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs6793123	0.83[AFR][1000 genomes]
rs6794273	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs73175407	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175433	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175435	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175442	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175449	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175451	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175463	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175491	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73177465	0.85[ASN][1000 genomes]
rs73177470	0.85[ASN][1000 genomes]
rs73177478	0.85[ASN][1000 genomes]
rs73177489	0.85[ASN][1000 genomes]
rs73177494	0.85[ASN][1000 genomes]
rs73179378	0.85[ASN][1000 genomes]
rs73179384	0.85[ASN][1000 genomes]
rs73181374	0.85[ASN][1000 genomes]
rs73181376	0.85[ASN][1000 genomes]
rs73181380	0.85[ASN][1000 genomes]
rs73181387	0.85[ASN][1000 genomes]
rs73181395	0.85[ASN][1000 genomes]
rs73181396	0.85[ASN][1000 genomes]
rs73181397	0.85[ASN][1000 genomes]
rs73181401	0.85[ASN][1000 genomes]
rs73183103	0.85[ASN][1000 genomes]
rs73183108	0.88[ASN][1000 genomes]
rs73183112	0.88[ASN][1000 genomes]
rs73183114	0.88[ASN][1000 genomes]
rs73183115	0.88[ASN][1000 genomes]
rs73183185	0.88[ASN][1000 genomes]
rs73183186	0.88[ASN][1000 genomes]
rs73183187	0.88[ASN][1000 genomes]
rs73183188	0.88[ASN][1000 genomes]
rs73183198	0.88[ASN][1000 genomes]
rs73185114	0.88[ASN][1000 genomes]
rs73185115	0.88[ASN][1000 genomes]
rs73189021	0.91[ASN][1000 genomes]
rs73189028	0.94[ASN][1000 genomes]
rs73189034	0.94[ASN][1000 genomes]
rs73189060	0.94[ASN][1000 genomes]
rs73192717	0.94[ASN][1000 genomes]
rs73192730	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192733	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192737	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192751	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73192754	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192770	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901280	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs978436	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv963527	chr3:105259211-105267049	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
5	chr3:105234600-105261000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:105237800-105274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:105237800-105275800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:105242000-105293600	Weak transcription	Lung	lung
10	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:105242800-105266800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:105244800-105275800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:105245800-105268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:105246600-105284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:105248000-105281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:105248200-105262800	Weak transcription	NHLF	lung
17	chr3:105248400-105291200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:105249400-105278600	Weak transcription	Small Intestine	intestine
19	chr3:105249800-105261200	Weak transcription	Fetal Intestine Small	intestine
20	chr3:105249800-105263400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:105249800-105284000	Weak transcription	Fetal Stomach	stomach
22	chr3:105249800-105285200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:105250600-105262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:105250600-105270400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:105251200-105266400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:105251800-105274400	Weak transcription	Dnd41	blood
27	chr3:105252600-105263400	Weak transcription	Left Ventricle	heart
28	chr3:105253200-105273000	Weak transcription	Gastric	stomach
29	chr3:105253800-105270000	Weak transcription	Fetal Intestine Large	intestine
30	chr3:105254000-105273000	Weak transcription	Fetal Lung	lung
31	chr3:105254800-105279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:105256200-105268200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:105257200-105269400	Weak transcription	Fetal Heart	heart
34	chr3:105257400-105272400	Weak transcription	NHDF-Ad	bronchial
35	chr3:105257800-105271400	Weak transcription	Stomach Mucosa	stomach
36	chr3:105258000-105270200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:105258000-105274600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:105258200-105263800	Strong transcription	HMEC	breast
39	chr3:105258200-105268400	Strong transcription	GM12878-XiMat	blood
40	chr3:105258600-105273600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:105258800-105260800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:105258800-105264800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:105258800-105266600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:105258800-105267000	Strong transcription	Primary B cells from cord blood	blood
45	chr3:105258800-105271800	Strong transcription	HUVEC	blood vessel
46	chr3:105258800-105274400	Strong transcription	Liver	Liver
47	chr3:105258800-105274400	Strong transcription	NH-A	brain
48	chr3:105259000-105261400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:105259000-105264000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:105259000-105264400	Strong transcription	Primary hematopoietic stem cells	blood

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