Variant report

Variant	rs2839690
Chromosome Location	chr10:44875166-44875167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:44874626..44876126-chr10:44876143..44877664,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11239031	0.95[EUR][1000 genomes]
rs11592974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11594377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11595460	0.93[EUR][1000 genomes]
rs17156193	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17540492	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17880777	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17883887	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17885289	0.84[AFR][1000 genomes]
rs2839679	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2839683	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2839686	0.90[LWK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs2839687	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2839689	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2839692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2839695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2861441	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2861442	0.90[LWK][hapmap];0.94[YRI][hapmap]
rs4087301	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4520554	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4556491	0.93[EUR][1000 genomes]
rs4556492	0.93[EUR][1000 genomes]
rs7082547	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7088876	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7092453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7093481	0.85[AFR][1000 genomes]
rs72790853	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72790854	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72790861	0.85[AFR][1000 genomes]
rs72790862	0.82[AFR][1000 genomes]
rs72790864	0.95[EUR][1000 genomes]
rs72790866	0.93[EUR][1000 genomes]
rs72790869	0.88[EUR][1000 genomes]
rs7915848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7918568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[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	nsv1054649	chr10:44848921-44889713	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv550699	chr10:44868257-44882203	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv895089	chr10:44874867-44880838	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv895090	chr10:44874867-44884959	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv895091	chr10:44875040-44888130	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv895092	chr10:44875166-44884959	Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44850600-44877600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr10:44860000-44879000	Weak transcription	Gastric	stomach
3	chr10:44864600-44876200	Weak transcription	Brain Anterior Caudate	brain
4	chr10:44864600-44876800	Strong transcription	Fetal Stomach	stomach
5	chr10:44864800-44877800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr10:44865400-44876200	Weak transcription	Right Atrium	heart
7	chr10:44865600-44878000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:44866000-44876200	Strong transcription	Left Ventricle	heart
9	chr10:44866000-44877600	Weak transcription	Fetal Brain Female	brain
10	chr10:44866200-44876000	Strong transcription	Osteobl	bone
11	chr10:44866400-44875600	Weak transcription	Fetal Brain Male	brain
12	chr10:44866400-44878600	Weak transcription	Liver	Liver
13	chr10:44866600-44876200	Weak transcription	Brain Germinal Matrix	brain
14	chr10:44866600-44877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:44866800-44875600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr10:44867000-44878200	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:44867400-44875200	Strong transcription	Ovary	ovary
18	chr10:44867400-44876000	Strong transcription	Adipose Nuclei	Adipose
19	chr10:44867400-44876400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:44867400-44878000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr10:44867600-44878600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:44867800-44875400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr10:44868000-44875600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr10:44869400-44875800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr10:44869600-44878200	Weak transcription	Brain Substantia Nigra	brain
26	chr10:44869800-44876000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr10:44870200-44877600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr10:44871000-44877600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:44871400-44875400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr10:44871600-44877000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:44871800-44877000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr10:44872000-44875600	Weak transcription	Colon Smooth Muscle	Colon
33	chr10:44872000-44875800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr10:44872400-44875600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:44872400-44877400	Weak transcription	Fetal Kidney	kidney
36	chr10:44872600-44875200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr10:44873000-44875800	Strong transcription	NHLF	lung
38	chr10:44873200-44875200	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr10:44873200-44875600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr10:44873200-44877600	Weak transcription	Lung	lung
41	chr10:44873400-44875200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:44873400-44875600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr10:44873400-44876200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr10:44873600-44876400	Strong transcription	NHDF-Ad	bronchial
45	chr10:44873600-44876600	Strong transcription	Fetal Lung	lung
46	chr10:44874200-44875400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:44874200-44875600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr10:44874400-44875200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr10:44874400-44877800	Weak transcription	Right Ventricle	heart
50	chr10:44874600-44875600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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