Variant report

Variant	rs13198780
Chromosome Location	chr6:15490017-15490018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15474184..15476635-chr6:15488076..15490844,2	K562	blood:
2	chr6:15483229..15486068-chr6:15489614..15491902,2	MCF-7	breast:
3	chr6:15489579..15491671-chr6:15507006..15508555,2	MCF-7	breast:
4	chr6:15243868..15248249-chr6:15486712..15491085,4	K562	blood:
5	chr6:15480753..15482538-chr6:15489895..15492218,2	K562	blood:
6	chr6:15478158..15480159-chr6:15489862..15492490,2	K562	blood:

Variant related genes	Relation type
ENSG00000271888	Chromatin interaction
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10949304	0.90[ASN][1000 genomes]
rs11964846	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966626	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13192234	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13192892	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13194650	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13196869	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13202100	0.88[EUR][1000 genomes]
rs13202955	0.88[EUR][1000 genomes]
rs13204842	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13208563	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13209668	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17455404	0.88[EUR][1000 genomes]
rs1967664	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076056	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237138	0.88[EUR][1000 genomes]
rs2299043	0.85[EUR][1000 genomes]
rs35868206	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3819396	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712251	0.90[EUR][1000 genomes]
rs4715975	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715979	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4715980	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899342	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899343	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6917591	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs742099	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs742100	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756331	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7761778	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769291	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7774429	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9383056	0.87[EUR][1000 genomes]
rs9383062	0.93[EUR][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	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15461600-15491000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:15471000-15502000	Weak transcription	A549	lung
3	chr6:15480400-15490600	Weak transcription	NHDF-Ad	bronchial
4	chr6:15481200-15491800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:15482200-15491400	Weak transcription	Fetal Brain Male	brain
6	chr6:15482400-15491400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:15483200-15490800	Weak transcription	HSMMtube	muscle
8	chr6:15483200-15491400	Weak transcription	Fetal Heart	heart
9	chr6:15484800-15496400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:15486200-15491000	Strong transcription	Primary B cells from cord blood	blood
11	chr6:15486200-15491400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:15486400-15490200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:15486400-15491600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:15486600-15490200	Strong transcription	Dnd41	blood
15	chr6:15486600-15491400	Weak transcription	Right Atrium	heart
16	chr6:15486800-15490800	Weak transcription	Psoas Muscle	Psoas
17	chr6:15486800-15502000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:15487000-15490400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr6:15487000-15490600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:15487000-15490800	Strong transcription	Fetal Stomach	stomach
21	chr6:15487200-15490200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:15487200-15490200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
23	chr6:15487200-15490200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:15487200-15490200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:15487200-15490200	Strong transcription	Brain Anterior Caudate	brain
26	chr6:15487200-15490400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:15487200-15491000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr6:15487200-15508000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr6:15487400-15490200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:15487400-15490200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:15487400-15490200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:15487400-15490200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:15487400-15490200	Strong transcription	Esophagus	oesophagus
34	chr6:15487400-15490200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:15487400-15490200	Strong transcription	Gastric	stomach
36	chr6:15487400-15490200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr6:15487400-15490800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:15487600-15490200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:15487600-15490200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:15487600-15490200	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr6:15487600-15490200	Strong transcription	Lung	lung
42	chr6:15487600-15490200	Strong transcription	Pancreas	Pancrea
43	chr6:15487600-15490400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:15487600-15490600	Strong transcription	Fetal Muscle Leg	muscle
45	chr6:15487600-15491000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:15488200-15490200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:15488200-15490200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:15488400-15490200	Genic enhancers	H1 Cell Line	embryonic stem cell
49	chr6:15488600-15491000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:15488800-15491800	Genic enhancers	HUES6 Cell Line	embryonic stem cell

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