Variant report

Variant	rs2278168
Chromosome Location	chr19:37038092-37038093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37038036..37040830-chr19:37176881..37179372,3	MCF-7	breast:
2	chr19:37028985..37031879-chr19:37035963..37038144,2	K562	blood:
3	chr19:37037541..37041127-chr19:37063019..37065545,3	K562	blood:
4	chr19:37017852..37021325-chr19:37033943..37038779,6	K562	blood:

Variant related genes	Relation type
ENSG00000189042	Chromatin interaction
ENSG00000228629	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000254004	Chromatin interaction
ENSG00000225975	Chromatin interaction
ENSG00000233527	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10414896	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234514	0.90[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs17238977	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2114287	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2912401	0.85[TSI][hapmap]
rs2912402	0.85[TSI][hapmap]
rs2967470	0.87[TSI][hapmap]
rs3096621	0.81[CEU][hapmap]
rs3108176	0.95[EUR][1000 genomes]
rs3108177	0.84[EUR][1000 genomes]
rs3108204	0.86[EUR][1000 genomes]
rs3108207	0.87[TSI][hapmap]
rs3108210	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs3108216	0.84[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs3108548	0.82[TSI][hapmap]
rs3108551	0.83[TSI][hapmap]
rs3108556	0.85[EUR][1000 genomes]
rs3108558	0.87[TSI][hapmap]
rs3108561	0.87[TSI][hapmap]
rs3108578	0.84[TSI][hapmap]
rs3108612	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs3170326	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745779	0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3760826	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57854762	0.90[EUR][1000 genomes]
rs61259689	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61396420	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61732180	0.93[EUR][1000 genomes]
rs62112474	0.94[EUR][1000 genomes]
rs62112477	0.92[EUR][1000 genomes]
rs62112481	0.88[EUR][1000 genomes]
rs7254978	0.87[TSI][hapmap]
rs73034161	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7343133	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8111881	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv1056134	chr19:37022039-37056943	Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2278168	TEX101	cis	cerebellum	SCAN
rs2278168	CEACAM20	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37021400-37061600	ZNF genes & repeats	Liver	Liver
2	chr19:37022800-37061200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:37023000-37061800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:37023200-37048400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:37023200-37060200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
6	chr19:37023200-37061600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:37023400-37048800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:37023400-37060000	ZNF genes & repeats	Fetal Lung	lung
9	chr19:37023400-37062000	ZNF genes & repeats	Fetal Brain Female	brain
10	chr19:37023400-37063000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:37023600-37061000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr19:37023800-37057800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:37023800-37058200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:37023800-37058200	ZNF genes & repeats	Dnd41	blood
15	chr19:37023800-37061600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:37025400-37052400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr19:37025600-37049000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
18	chr19:37025600-37053000	ZNF genes & repeats	Brain Anterior Caudate	brain
19	chr19:37025600-37061000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr19:37025600-37062800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:37025800-37048000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:37025800-37048400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
23	chr19:37025800-37060200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
24	chr19:37027400-37054400	ZNF genes & repeats	Brain Hippocampus Middle	brain
25	chr19:37027600-37049200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
26	chr19:37028200-37045800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:37028600-37050800	ZNF genes & repeats	Primary B cells from cord blood	blood
28	chr19:37028600-37055000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr19:37028600-37061800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
30	chr19:37028800-37048800	ZNF genes & repeats	Brain Substantia Nigra	brain
31	chr19:37028800-37054400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
32	chr19:37029000-37060000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
33	chr19:37030600-37048600	ZNF genes & repeats	Brain Germinal Matrix	brain
34	chr19:37031400-37047800	ZNF genes & repeats	Colon Smooth Muscle	Colon
35	chr19:37031400-37049600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
36	chr19:37031400-37056800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
37	chr19:37031400-37057800	ZNF genes & repeats	Primary T cells from cord blood	blood
38	chr19:37032800-37048000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
39	chr19:37033400-37047800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
40	chr19:37033400-37048400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
41	chr19:37033400-37051000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:37033600-37042200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
43	chr19:37033600-37048000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:37033600-37048600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
45	chr19:37033800-37043000	ZNF genes & repeats	Fetal Heart	heart
46	chr19:37033800-37047600	ZNF genes & repeats	Fetal Kidney	kidney
47	chr19:37033800-37048000	ZNF genes & repeats	HSMMtube	muscle
48	chr19:37033800-37048400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
49	chr19:37034000-37054000	ZNF genes & repeats	A549	lung
50	chr19:37034000-37063000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links