Variant report

Variant	rs3768239
Chromosome Location	chr1:85154209-85154210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85153044..85155913-chr1:85168206..85170903,2	K562	blood:
2	chr1:85151664..85154712-chr1:85171325..85174497,4	K562	blood:
3	chr1:85152648..85155097-chr1:85155098..85157489,2	MCF-7	breast:
4	chr1:85150908..85155231-chr1:85184814..85188587,5	K562	blood:

Variant related genes	Relation type
ENSG00000117155	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10465723	0.93[ASN][1000 genomes]
rs1057746	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs10874453	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10874454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11161435	0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11161436	0.90[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11164031	0.88[ASN][1000 genomes]
rs11164032	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11164033	0.91[ASN][1000 genomes]
rs11164034	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs11164036	0.97[ASN][1000 genomes]
rs11164041	0.99[ASN][1000 genomes]
rs11164048	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12044089	0.89[ASN][1000 genomes]
rs12049262	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12137124	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs12730273	0.99[ASN][1000 genomes]
rs12736243	0.87[ASN][1000 genomes]
rs2911561	0.84[ASN][1000 genomes]
rs2911562	0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs2911563	0.80[ASN][1000 genomes]
rs2911564	0.88[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2911565	0.86[ASN][1000 genomes]
rs2911566	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3118466	0.92[ASN][1000 genomes]
rs3768240	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768241	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768242	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3768243	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs4537578	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs4907086	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57636989	0.93[ASN][1000 genomes]
rs6681911	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs7524511	0.87[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs7550108	0.91[ASN][1000 genomes]
rs818524	0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947283	chr1:85150944-85155058	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3768239	COL24A1	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85106400-85155400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:85108000-85155000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:85124600-85154400	Weak transcription	A549	lung
4	chr1:85126400-85154800	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:85126400-85155200	Weak transcription	Left Ventricle	heart
6	chr1:85126600-85154400	Weak transcription	Fetal Stomach	stomach
7	chr1:85127800-85154400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:85138000-85154800	Weak transcription	HSMMtube	muscle
9	chr1:85138800-85155000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:85143600-85154600	Weak transcription	Primary B cells from cord blood	blood
11	chr1:85144400-85154400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:85151400-85154400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:85152000-85155000	Active TSS	Brain Angular Gyrus	brain
14	chr1:85152400-85154800	Weak transcription	Aorta	Aorta
15	chr1:85152600-85154400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:85152600-85156800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:85152800-85154400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:85152800-85155200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:85153000-85154400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:85153000-85155000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:85153200-85154400	Enhancers	Dnd41	blood
22	chr1:85153200-85154800	Enhancers	HepG2	liver
23	chr1:85153200-85155000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:85153200-85155200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr1:85153400-85154400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:85153400-85154400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:85153400-85154400	Enhancers	Small Intestine	intestine
28	chr1:85153400-85154600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:85153400-85154600	Enhancers	Liver	Liver
30	chr1:85153400-85154800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:85153400-85154800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:85153400-85155000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:85153600-85154400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:85153600-85154400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:85153600-85154400	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:85153600-85154400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr1:85153600-85154400	Enhancers	Fetal Kidney	kidney
38	chr1:85153600-85154600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr1:85153600-85154600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:85153600-85154600	Enhancers	Rectal Smooth Muscle	rectum
41	chr1:85153600-85154600	Flanking Active TSS	NHLF	lung
42	chr1:85153600-85154800	Flanking Active TSS	Fetal Brain Male	brain
43	chr1:85153600-85155000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:85153600-85155000	Enhancers	Fetal Heart	heart
45	chr1:85153600-85155200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:85153600-85157000	Active TSS	K562	blood
47	chr1:85153600-85157400	Active TSS	Stomach Smooth Muscle	stomach
48	chr1:85153800-85154400	Enhancers	Hela-S3	cervix
49	chr1:85153800-85154400	Enhancers	NH-A	brain
50	chr1:85153800-85154800	Flanking Active TSS	NHDF-Ad	bronchial

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