Variant report

Variant	rs11174498
Chromosome Location	chr12:62865345-62865346
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	chr12:62829632..62831889-chr12:62864077..62865718,2	MCF-7	breast:
2	chr12:62858973..62862705-chr12:62864289..62872208,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000061987	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10877855	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877856	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877857	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877859	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877862	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877864	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877870	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174487	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11174494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174496	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174504	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174514	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174517	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174518	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174527	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174537	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11174557	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174562	0.82[AFR][1000 genomes]
rs11174568	0.91[AFR][1000 genomes]
rs11174571	0.91[AFR][1000 genomes]
rs11174575	0.91[AFR][1000 genomes]
rs11520127	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613132	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11614022	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614822	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367878	0.91[AFR][1000 genomes]
rs12369751	0.91[AFR][1000 genomes]
rs12369961	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12369985	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370404	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17731893	0.82[AFR][1000 genomes]
rs17732089	0.82[AFR][1000 genomes]
rs17732182	0.91[AFR][1000 genomes]
rs55833440	0.82[AFR][1000 genomes]
rs7296573	0.91[AFR][1000 genomes]
rs7297093	0.91[AFR][1000 genomes]
rs7301016	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302094	0.91[AFR][1000 genomes]
rs7302456	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303825	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124315	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73126004	0.82[AFR][1000 genomes]
rs73126024	0.91[AFR][1000 genomes]
rs73141014	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73141045	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962519	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975109	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62861600-62865800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:62861600-62866600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:62861800-62879800	Weak transcription	HSMMtube	muscle
4	chr12:62861800-62902200	Weak transcription	Fetal Kidney	kidney
5	chr12:62862800-62867200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:62862800-62895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:62863000-62869400	Weak transcription	Fetal Intestine Small	intestine
8	chr12:62863200-62865600	Weak transcription	Right Ventricle	heart
9	chr12:62863200-62865800	Weak transcription	Aorta	Aorta
10	chr12:62863200-62866000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:62863200-62866000	Weak transcription	NHLF	lung
12	chr12:62863200-62866200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:62863200-62866200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:62863200-62870400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:62863200-62870600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:62863200-62870600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:62863200-62871000	Weak transcription	Placenta	Placenta
18	chr12:62863200-62871000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:62863200-62871200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:62863200-62875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:62863200-62875600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:62863200-62875600	Weak transcription	Gastric	stomach
23	chr12:62863200-62876000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:62863200-62879400	Weak transcription	Thymus	Thymus
25	chr12:62863200-62881400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:62863200-62895200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr12:62863200-62896800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:62863200-62901800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:62863200-62937400	Weak transcription	Pancreas	Pancrea
30	chr12:62863400-62865600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:62863400-62865800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:62863400-62866000	Weak transcription	NHDF-Ad	bronchial
33	chr12:62863400-62866200	Weak transcription	Fetal Heart	heart
34	chr12:62863400-62870600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:62863400-62870600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:62863400-62870800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:62863400-62870800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:62863400-62871400	Weak transcription	Fetal Brain Male	brain
39	chr12:62863400-62871400	Weak transcription	Osteobl	bone
40	chr12:62863400-62874000	Weak transcription	Hela-S3	cervix
41	chr12:62863400-62875600	Weak transcription	Brain Angular Gyrus	brain
42	chr12:62863400-62877600	Weak transcription	A549	lung
43	chr12:62863400-62878200	Weak transcription	Fetal Lung	lung
44	chr12:62863400-62895400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:62863400-62902000	Weak transcription	HUVEC	blood vessel
46	chr12:62863400-62911000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:62863600-62865400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:62863600-62865400	Weak transcription	GM12878-XiMat	blood
49	chr12:62863600-62870600	Weak transcription	HepG2	liver
50	chr12:62863600-62874200	Weak transcription	Brain Substantia Nigra	brain

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