Variant report

Variant	rs12254798
Chromosome Location	chr10:43955430-43955431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43889454..43895016-chr10:43953657..43957344,5	MCF-7	breast:
2	chr10:43899870..43905980-chr10:43953401..43957689,7	MCF-7	breast:
3	chr10:43949801..43952727-chr10:43954596..43956488,2	K562	blood:
4	chr10:43887055..43906178-chr10:43946385..43955803,85	K562	blood:

Variant related genes	Relation type
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10409	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899791	0.81[ASN][1000 genomes]
rs10899793	0.81[ASN][1000 genomes]
rs10899796	0.85[ASN][1000 genomes]
rs10899800	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899801	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899802	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899803	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899806	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899807	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899808	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11238530	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11238532	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11238536	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11238553	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238558	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238566	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238572	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11525297	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11815101	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12220230	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12220528	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12245541	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12250140	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12261855	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12262836	0.88[AMR][1000 genomes]
rs13376803	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13376924	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17153534	0.81[ASN][1000 genomes]
rs28865415	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4648316	0.81[ASN][1000 genomes]
rs59383062	0.81[ASN][1000 genomes]
rs59806733	0.81[ASN][1000 genomes]
rs7099802	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7907179	0.84[AMR][1000 genomes];0.88[ASN][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	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1043746	chr10:43940898-43977155	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43951800-43957400	Weak transcription	Fetal Kidney	kidney
2	chr10:43952000-43956400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:43952000-43957000	Weak transcription	K562	blood
4	chr10:43952000-43957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:43952000-43957600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr10:43952000-43957600	Weak transcription	Brain Anterior Caudate	brain
7	chr10:43952000-43957600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:43952000-43957600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:43952000-43957600	Weak transcription	Hela-S3	cervix
10	chr10:43952000-43960000	Weak transcription	Left Ventricle	heart
11	chr10:43952000-43972600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr10:43952000-43973200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr10:43952000-43977200	Weak transcription	HSMMtube	muscle
14	chr10:43952200-43956200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:43952200-43956800	Weak transcription	NHEK	skin
16	chr10:43952200-43957000	Weak transcription	Spleen	Spleen
17	chr10:43952200-43957200	Weak transcription	Fetal Intestine Small	intestine
18	chr10:43952200-43957400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:43952200-43957400	Weak transcription	Brain Hippocampus Middle	brain
20	chr10:43952200-43957600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:43952200-43957600	Weak transcription	Adipose Nuclei	Adipose
22	chr10:43952200-43957600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr10:43952200-43957600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr10:43952200-43961600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr10:43952200-43967800	Weak transcription	Right Atrium	heart
26	chr10:43952200-43975200	Weak transcription	Fetal Stomach	stomach
27	chr10:43952400-43956800	Weak transcription	HepG2	liver
28	chr10:43952400-43957200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr10:43952400-43976200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:43952600-43957200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr10:43952600-43957200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr10:43952600-43957200	Weak transcription	Dnd41	blood
33	chr10:43952600-43957800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:43952600-43967400	Weak transcription	Fetal Muscle Leg	muscle
35	chr10:43952800-43957200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr10:43952800-43957200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr10:43952800-43957200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:43952800-43957400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr10:43952800-43957400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr10:43952800-43957600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr10:43952800-43957600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr10:43952800-43957600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:43953000-43957400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr10:43954400-43957400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr10:43954400-43957400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr10:43954400-43960400	Weak transcription	Primary T cells from cord blood	blood
47	chr10:43954600-43957600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr10:43954800-43959200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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