Variant report

Variant	rs16846593
Chromosome Location	chr1:173898217-173898218
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173834350..173837246-chr1:173897897..173899668,2	K562	blood:
2	chr1:173894161..173896195-chr1:173897803..173900471,2	K562	blood:
3	chr1:173893484..173896039-chr1:173897096..173899356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234741	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16846433	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs16846526	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16846546	0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs16846561	0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs2065170	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2068871	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs2146372	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2227589	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2227592	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2759328	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs3791022	0.83[JPT][hapmap]
rs58174255	0.98[ASN][1000 genomes]
rs58911640	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59393482	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs60689957	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6685043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7516351	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7521960	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941987	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs941988	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
3	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv3407396	chr1:173896346-173917122	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16846593	RABGAP1L	cis	lymphoblastoid	seeQTL
rs16846593	CENPL	cis	lymphoblastoid	seeQTL
rs16846593	dJ383J4.3	cis	multi-tissue	Pritchard

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
3	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
4	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
5	chr1:173874400-173899800	Weak transcription	Primary T cells from cord blood	blood
6	chr1:173879200-173899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:173882800-173912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:173888400-173900200	Weak transcription	Right Atrium	heart
9	chr1:173891200-173899400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:173893400-173908400	Weak transcription	Colonic Mucosa	Colon
11	chr1:173894000-173904800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:173894400-173905000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:173894600-173899200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:173894600-173907800	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:173894600-173914400	Weak transcription	Right Ventricle	heart
16	chr1:173895000-173902400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:173895000-173903400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:173895200-173900000	Weak transcription	A549	lung
19	chr1:173895200-173912200	Weak transcription	Stomach Mucosa	stomach
20	chr1:173895400-173900000	Weak transcription	K562	blood
21	chr1:173895400-173907600	Weak transcription	Ovary	ovary
22	chr1:173895600-173901200	Weak transcription	HUVEC	blood vessel
23	chr1:173895600-173906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:173895800-173906200	Weak transcription	HepG2	liver
25	chr1:173896000-173899400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:173896000-173899600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:173896400-173901400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:173896400-173902800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:173896400-173907800	Weak transcription	Gastric	stomach
30	chr1:173896400-173910000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:173896400-173914400	Weak transcription	Pancreas	Pancrea
32	chr1:173896600-173899400	Weak transcription	Fetal Intestine Large	intestine
33	chr1:173896600-173902800	Weak transcription	Adipose Nuclei	Adipose
34	chr1:173896800-173908400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:173897000-173907800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:173897000-173908400	Weak transcription	Fetal Intestine Small	intestine
37	chr1:173897200-173899600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:173897400-173899400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:173897400-173907200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:173897600-173898800	Enhancers	Liver	Liver
41	chr1:173897600-173899800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:173897600-173900000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:173897600-173903600	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:173897600-173907200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:173897800-173899400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:173897800-173899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:173897800-173899400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:173897800-173899400	Weak transcription	Esophagus	oesophagus
49	chr1:173897800-173900000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:173897800-173900000	Weak transcription	Rectal Mucosa Donor 31	rectum

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