Variant report

Variant	rs11239020
Chromosome Location	chr10:44863993-44863994
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:44858744..44861385-chr10:44862420..44864353,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1065297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10793537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10900028	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10900030	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];0.94[ASN][1000 genomes]
rs10900031	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239019	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];0.94[ASN][1000 genomes]
rs11239021	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];0.94[ASN][1000 genomes]
rs11239032	0.88[ASN][1000 genomes]
rs12258838	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];0.94[ASN][1000 genomes]
rs12357238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17540465	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17878782	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17881412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17881729	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17887234	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1804429	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];0.94[ASN][1000 genomes]
rs1804430	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];0.94[ASN][1000 genomes]
rs1889401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1889402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2105397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2839696	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];0.94[ASN][1000 genomes]
rs4948878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59675227	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60357795	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038511	chr10:44596885-44870030	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1052337	chr10:44821390-44865015	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44838600-44867400	Weak transcription	Spleen	Spleen
2	chr10:44848200-44864600	Weak transcription	Fetal Kidney	kidney
3	chr10:44848200-44865000	Weak transcription	Osteobl	bone
4	chr10:44848400-44865000	Weak transcription	Right Atrium	heart
5	chr10:44848400-44867400	Weak transcription	Adipose Nuclei	Adipose
6	chr10:44848400-44867600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:44849400-44869000	Weak transcription	Right Ventricle	heart
8	chr10:44849800-44864800	Weak transcription	Left Ventricle	heart
9	chr10:44850600-44877600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr10:44854000-44865800	Weak transcription	Fetal Intestine Small	intestine
11	chr10:44854200-44867200	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:44854400-44869000	Weak transcription	Brain Substantia Nigra	brain
13	chr10:44856200-44865000	Weak transcription	Aorta	Aorta
14	chr10:44858000-44864200	Strong transcription	Fetal Stomach	stomach
15	chr10:44858600-44864600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:44858800-44866600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr10:44859000-44864200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:44859000-44864800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr10:44859000-44865000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr10:44859000-44865000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr10:44859000-44871800	Weak transcription	Psoas Muscle	Psoas
22	chr10:44859200-44864200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr10:44859200-44864600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:44859800-44864600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr10:44860000-44879000	Weak transcription	Gastric	stomach
26	chr10:44860200-44864400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:44860200-44864600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:44860200-44868800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr10:44861400-44869200	Weak transcription	Colonic Mucosa	Colon
30	chr10:44862000-44866400	Genic enhancers	Fetal Muscle Leg	muscle
31	chr10:44862200-44866400	Weak transcription	Brain Germinal Matrix	brain
32	chr10:44862600-44865200	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr10:44862600-44865200	Weak transcription	Ovary	ovary
34	chr10:44862600-44865400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr10:44863000-44864800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:44863000-44867400	Weak transcription	Pancreas	Pancrea
37	chr10:44863200-44864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr10:44863200-44869400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr10:44863600-44864600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr10:44863600-44866400	Enhancers	Fetal Lung	lung

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