Variant report

Variant	rs12258838
Chromosome Location	chr10:44868465-44868466
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	chr10:44856118..44857833-chr10:44865837..44868542,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1029153	0.80[YRI][hapmap]
rs1065297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900028	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs10900031	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];1.00[ASN][1000 genomes]
rs11239016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs11239020	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];1.00[ASN][1000 genomes]
rs11239032	0.94[ASN][1000 genomes]
rs12357238	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17540465	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17878782	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881729	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17887234	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1804429	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[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];1.00[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];1.00[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];1.00[ASN][1000 genomes]
rs1889402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760669	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[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];1.00[ASN][1000 genomes]
rs4948878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59675227	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60357795	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	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
3	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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44849400-44869000	Weak transcription	Right Ventricle	heart
2	chr10:44850600-44877600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr10:44854400-44869000	Weak transcription	Brain Substantia Nigra	brain
4	chr10:44859000-44871800	Weak transcription	Psoas Muscle	Psoas
5	chr10:44860000-44879000	Weak transcription	Gastric	stomach
6	chr10:44860200-44868800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:44861400-44869200	Weak transcription	Colonic Mucosa	Colon
8	chr10:44863200-44869400	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr10:44864600-44871600	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:44864600-44876200	Weak transcription	Brain Anterior Caudate	brain
11	chr10:44864600-44876800	Strong transcription	Fetal Stomach	stomach
12	chr10:44864800-44877800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:44865000-44873000	Weak transcription	Esophagus	oesophagus
14	chr10:44865200-44868600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr10:44865400-44876200	Weak transcription	Right Atrium	heart
16	chr10:44865600-44878000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr10:44865800-44872200	Strong transcription	Fetal Intestine Small	intestine
18	chr10:44866000-44876200	Strong transcription	Left Ventricle	heart
19	chr10:44866000-44877600	Weak transcription	Fetal Brain Female	brain
20	chr10:44866200-44876000	Strong transcription	Osteobl	bone
21	chr10:44866400-44868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:44866400-44870000	Strong transcription	Fetal Muscle Leg	muscle
23	chr10:44866400-44875600	Weak transcription	Fetal Brain Male	brain
24	chr10:44866400-44878600	Weak transcription	Liver	Liver
25	chr10:44866600-44870600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr10:44866600-44876200	Weak transcription	Brain Germinal Matrix	brain
27	chr10:44866600-44877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:44866800-44871800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr10:44866800-44875600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr10:44867000-44872200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:44867000-44878200	Weak transcription	Brain Hippocampus Middle	brain
32	chr10:44867200-44872000	Strong transcription	Colon Smooth Muscle	Colon
33	chr10:44867200-44872000	Strong transcription	Fetal Lung	lung
34	chr10:44867400-44868800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr10:44867400-44868800	Strong transcription	Pancreas	Pancrea
36	chr10:44867400-44869600	Strong transcription	Aorta	Aorta
37	chr10:44867400-44871000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:44867400-44871800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr10:44867400-44875200	Strong transcription	Ovary	ovary
40	chr10:44867400-44876000	Strong transcription	Adipose Nuclei	Adipose
41	chr10:44867400-44876400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr10:44867400-44878000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr10:44867600-44871600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:44867600-44878600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr10:44867800-44871400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr10:44867800-44872400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr10:44867800-44875400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr10:44868000-44869600	Strong transcription	Fetal Kidney	kidney
49	chr10:44868000-44869600	Strong transcription	NHLF	lung
50	chr10:44868000-44869800	Strong transcription	Spleen	Spleen

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