Variant report

Variant	rs2789488
Chromosome Location	chr6:149725290-149725291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs2143076	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2179367	0.86[EUR][1000 genomes]
rs2262617	0.85[EUR][1000 genomes]
rs2341783	0.87[JPT][hapmap]
rs2341784	0.87[JPT][hapmap]
rs2744427	0.87[JPT][hapmap]
rs2744432	0.82[AMR][1000 genomes]
rs2744434	0.87[JPT][hapmap]
rs2789490	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2789492	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789500	0.87[JPT][hapmap]
rs3734296	0.87[JPT][hapmap]
rs472810	0.85[JPT][hapmap]
rs474369	0.87[JPT][hapmap]
rs478767	0.87[JPT][hapmap]
rs480526	0.86[JPT][hapmap]
rs489551	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4895788	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4895789	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs4897124	0.85[EUR][1000 genomes]
rs4897125	0.83[EUR][1000 genomes]
rs492956	0.85[JPT][hapmap]
rs494340	0.82[JPT][hapmap]
rs501926	0.87[JPT][hapmap]
rs504762	0.82[JPT][hapmap]
rs504985	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs506268	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511100	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs511105	0.87[JPT][hapmap]
rs514839	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs515133	0.83[JPT][hapmap]
rs521845	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs532250	0.83[JPT][hapmap]
rs536203	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs537354	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs538386	0.87[JPT][hapmap]
rs540538	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs544947	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556335	0.87[JPT][hapmap]
rs559052	0.86[JPT][hapmap]
rs560051	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs562428	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs564961	0.92[ASN][1000 genomes]
rs565825	0.86[JPT][hapmap]
rs570442	0.82[JPT][hapmap]
rs577001	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs579789	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs580011	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs585022	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs600739	0.81[JPT][hapmap]
rs628488	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs638407	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs652807	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs652921	0.87[JPT][hapmap]
rs6570965	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs663625	0.87[JPT][hapmap]
rs909793	0.90[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs9285519	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9322178	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9373589	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9373592	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9377212	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9377218	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9390676	0.86[JPT][hapmap]
rs9390677	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9404034	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv969455	chr6:149720845-149727255	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149687800-149726400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:149700400-149728400	Weak transcription	Hela-S3	cervix
3	chr6:149700400-149732400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:149700600-149730800	Weak transcription	Fetal Brain Male	brain
5	chr6:149700800-149732800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:149701400-149730800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:149701400-149734200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:149701600-149733600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:149703400-149730600	Weak transcription	Brain Germinal Matrix	brain
10	chr6:149703600-149730400	Weak transcription	NHLF	lung
11	chr6:149705200-149734600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:149709400-149733000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:149709600-149729800	Weak transcription	Fetal Heart	heart
14	chr6:149709600-149750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:149711400-149726000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr6:149711400-149726600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr6:149712000-149727200	Strong transcription	Primary hematopoietic stem cells	blood
18	chr6:149713800-149735400	Weak transcription	Small Intestine	intestine
19	chr6:149714000-149728000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:149714800-149730800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:149715000-149728200	Strong transcription	Fetal Thymus	thymus
22	chr6:149715400-149732600	Strong transcription	Dnd41	blood
23	chr6:149715600-149733600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:149716000-149728000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:149716000-149728200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:149716400-149728600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:149717200-149726400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr6:149717200-149726800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:149717400-149726200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:149717400-149726200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:149717400-149726600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:149717400-149728200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:149717400-149728400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:149717400-149733200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:149717600-149727000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:149717600-149727600	Strong transcription	Primary B cells from cord blood	blood
37	chr6:149717800-149732200	Strong transcription	GM12878-XiMat	blood
38	chr6:149718600-149727200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:149718600-149727800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:149718800-149727200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:149718800-149727600	Weak transcription	Stomach Mucosa	stomach
42	chr6:149718800-149727800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:149718800-149728400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:149718800-149732800	Strong transcription	HSMM	muscle
45	chr6:149719000-149727400	Strong transcription	NH-A	brain
46	chr6:149720200-149727800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:149720400-149726600	Strong transcription	Liver	Liver
48	chr6:149720800-149726400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:149721600-149726400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:149721600-149726600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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