Variant report

Variant	rs269990
Chromosome Location	chr6:128107342-128107343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1342649	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1445644	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs172008	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs269991	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269996	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs269999	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs270001	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs270002	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs270003	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs270007	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs270008	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs270011	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs270013	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs270014	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs270015	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2780929	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34471518	0.84[AMR][1000 genomes]
rs35158225	0.84[AMR][1000 genomes]
rs440576	1.00[CEU][hapmap]
rs486235	0.83[AMR][1000 genomes]
rs490008	0.80[AMR][1000 genomes]
rs583072	0.80[AMR][1000 genomes]
rs614885	0.80[AMR][1000 genomes]
rs648151	0.80[AMR][1000 genomes]
rs655681	0.80[AMR][1000 genomes]
rs67116440	0.80[AMR][1000 genomes]
rs683202	0.83[AMR][1000 genomes]
rs6921729	1.00[CEU][hapmap];0.85[EUR][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	nsv886639	chr6:127954614-128109244	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv886643	chr6:127971136-128109244	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv886644	chr6:127976408-128109244	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv886647	chr6:127977160-128109244	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv886648	chr6:127983009-128109244	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv830799	chr6:128033100-128194511	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128101800-128110000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:128103000-128111800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:128103600-128113800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:128103800-128108200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:128104000-128107600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:128104000-128108000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:128104400-128113400	Weak transcription	Dnd41	blood
8	chr6:128105600-128107400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:128105800-128107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:128105800-128107800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:128105800-128108000	Weak transcription	Thymus	Thymus
12	chr6:128106000-128107400	Weak transcription	Primary T cells from cord blood	blood
13	chr6:128106000-128107400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:128106000-128107600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:128106000-128107800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:128106000-128108000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:128106000-128114000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:128106200-128107400	Weak transcription	Fetal Thymus	thymus
19	chr6:128106200-128113600	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:128106400-128107800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:128106800-128108600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:128107000-128108200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:128107000-128108200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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