Variant report

Variant	rs12200013
Chromosome Location	chr6:39178783-39178784
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39178389..39182010-chr6:39186397..39189185,3	MCF-7	breast:
2	chr6:39160517..39162848-chr6:39178719..39180360,2	MCF-7	breast:
3	chr6:39172344..39173847-chr6:39177275..39179261,2	K562	blood:
4	chr6:39176890..39181297-chr6:39193958..39200095,7	K562	blood:
5	chr6:39176203..39179495-chr6:39195269..39198252,3	MCF-7	breast:
6	chr6:39177427..39182769-chr6:39182785..39188256,10	K562	blood:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10807202	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947786	0.82[ASN][1000 genomes]
rs10947787	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947788	0.92[ASN][1000 genomes]
rs10947789	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190363	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12202900	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12207689	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033226	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711585	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714223	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714224	0.88[ASN][1000 genomes]
rs55818834	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918122	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72851851	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
2	chr6:39156800-39193400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:39163800-39192800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:39169400-39193600	Enhancers	Liver	Liver
5	chr6:39170000-39179400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr6:39170400-39179200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr6:39170800-39179200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:39171000-39179200	Genic enhancers	K562	blood
9	chr6:39171400-39179200	Enhancers	Esophagus	oesophagus
10	chr6:39174000-39179000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:39174000-39179200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:39174000-39179400	Enhancers	Fetal Lung	lung
13	chr6:39174200-39195000	Enhancers	Stomach Mucosa	stomach
14	chr6:39174600-39178800	Enhancers	Fetal Intestine Large	intestine
15	chr6:39175200-39179400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:39175600-39178800	Enhancers	Colonic Mucosa	Colon
17	chr6:39175800-39179200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:39175800-39179400	Enhancers	Pancreas	Pancrea
19	chr6:39176000-39179200	Enhancers	Fetal Muscle Trunk	muscle
20	chr6:39177000-39179200	Enhancers	H9 Cell Line	embryonic stem cell
21	chr6:39177000-39179400	Enhancers	Adipose Nuclei	Adipose
22	chr6:39177000-39179600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr6:39177000-39179600	Enhancers	Spleen	Spleen
24	chr6:39177000-39180400	Enhancers	Ovary	ovary
25	chr6:39177600-39179000	Weak transcription	Gastric	stomach
26	chr6:39177600-39181000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:39177600-39182200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:39177600-39182800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:39177600-39186400	Weak transcription	Primary T cells from cord blood	blood
30	chr6:39177800-39180400	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:39177800-39182200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:39177800-39183400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:39178000-39180600	Weak transcription	A549	lung
34	chr6:39178000-39181000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:39178000-39182000	Weak transcription	Fetal Kidney	kidney
36	chr6:39178000-39183400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:39178000-39193400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:39178200-39179000	Enhancers	Fetal Thymus	thymus
39	chr6:39178200-39179400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr6:39178200-39180000	Weak transcription	Fetal Stomach	stomach
41	chr6:39178200-39180800	Weak transcription	Primary B cells from cord blood	blood
42	chr6:39178200-39181800	Weak transcription	Placenta	Placenta
43	chr6:39178200-39182800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr6:39178200-39183000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr6:39178200-39184400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:39178200-39185000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:39178200-39185000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:39178200-39185200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:39178200-39186600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:39178400-39178800	Weak transcription	Primary hematopoietic stem cells	blood

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