Variant report

Variant	rs3789608
Chromosome Location	chr1:114397788-114397789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114391438..114393621-chr1:114396870..114398457,3	MCF-7	breast:
2	chr1:114352745..114355342-chr1:114397110..114401660,4	MCF-7	breast:
3	chr1:114396276..114399054-chr1:114408644..114411228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231128	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11582409	0.85[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584821	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17031795	0.84[ASN][1000 genomes]
rs17463292	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17509844	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17510162	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3195954	0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34122108	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35173468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761935	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765598	0.94[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789604	0.80[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3811021	0.94[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3827733	0.94[CHB][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4393155	0.86[ASN][1000 genomes]
rs4589108	0.84[ASN][1000 genomes]
rs4839000	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs4839333	0.82[CHB][hapmap]
rs4839341	0.84[ASN][1000 genomes]
rs4839346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55646484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55940960	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55951516	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6658523	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700802	0.85[YRI][hapmap];0.82[AFR][1000 genomes]

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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114355000-114401000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:114355000-114401000	Weak transcription	Spleen	Spleen
3	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:114378000-114402600	Weak transcription	Colonic Mucosa	Colon
5	chr1:114390800-114400200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:114391200-114401800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:114393600-114399400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:114394200-114399200	Strong transcription	GM12878-XiMat	blood
9	chr1:114394400-114402200	Strong transcription	Primary T cells from cord blood	blood
10	chr1:114395800-114398600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:114396400-114400800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:114396600-114399400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:114396600-114401600	Strong transcription	Thymus	Thymus
14	chr1:114396800-114397800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:114396800-114399200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:114396800-114399400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:114396800-114399400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:114396800-114401600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:114396800-114401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:114396800-114402000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:114396800-114402000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:114396800-114402200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr1:114397000-114397800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:114397000-114399200	Strong transcription	Primary B cells from cord blood	blood
25	chr1:114397000-114399400	Strong transcription	Primary hematopoietic stem cells	blood
26	chr1:114397000-114400000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:114397000-114401600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:114397000-114401800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:114397000-114401800	Strong transcription	Fetal Thymus	thymus
30	chr1:114397000-114402400	Strong transcription	Dnd41	blood
31	chr1:114397200-114397800	Genic enhancers	Monocytes-CD14+_RO01746	blood
32	chr1:114397200-114399600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:114397400-114397800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:114397400-114402000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr1:114397600-114399000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:114397600-114402600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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