Variant report

Variant	rs12749
Chromosome Location	chr1:151555741-151555742
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151511523..151514176-chr1:151553602..151559967,11	MCF-7	breast:
2	1:151478607-151483211..1:151554759-151560153	Hela-S3	cervix:
3	chr1:151517397..151520061-chr1:151554421..151557663,3	MCF-7	breast:
4	chr1:151555489..151558097-chr1:151879196..151882038,2	MCF-7	breast:
5	chr1:151430481..151432221-chr1:151554534..151556379,2	MCF-7	breast:
6	chr1:151430408..151432425-chr1:151553312..151556210,2	MCF-7	breast:
7	1:151496437-151509688..1:151554759-151560153	Hela-S3	cervix:
8	chr1:151518179..151521710-chr1:151554495..151558712,6	MCF-7	breast:
9	chr1:151553336..151556104-chr17:57915275..57918258,2	MCF-7	breast:
10	chr1:151554350..151557828-chr1:151561195..151563767,4	K562	blood:
11	1:151554759-151560153..1:151618750-151636526	Hela-S3	cervix:
12	chr1:151555047..151557033-chr1:151584735..151586308,2	MCF-7	breast:
13	chr1:151510996..151514435-chr1:151551077..151556153,9	MCF-7	breast:
14	1:151411623-151426875..1:151554759-151560153	Hela-S3	cervix:
15	chr1:151539684..151544323-chr1:151552691..151557234,8	MCF-7	breast:
16	chr1:151539929..151545457-chr1:151553538..151558687,9	MCF-7	breast:
17	chr1:151549748..151551460-chr1:151553412..151555994,2	K562	blood:
18	chr1:151553739..151556005-chr1:151563177..151565772,3	MCF-7	breast:
19	chr1:151506703..151509492-chr1:151555200..151556756,2	MCF-7	breast:
20	1:151516085-151535167..1:151554759-151560153	Hela-S3	cervix:
21	chr1:151555396..151557828-chr1:151561195..151563798,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143367	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000250734	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000252840	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10888424	0.90[EUR][1000 genomes]
rs1539492	0.90[MEX][hapmap]
rs1970568	0.93[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs6587606	0.93[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6698868	0.90[EUR][1000 genomes]
rs6701819	0.90[MEX][hapmap]
rs7528601	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12749	LINGO4	cis	cerebellum	SCAN
rs12749	IVL	cis	cerebellum	SCAN
rs12749	CGN	cis	parietal	SCAN
rs12749	BOD1P	trans	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151514400-151556800	Weak transcription	Fetal Brain Male	brain
2	chr1:151521800-151559000	Weak transcription	Small Intestine	intestine
3	chr1:151533000-151557200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:151533800-151561600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:151535800-151561800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:151537000-151556800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:151537400-151556000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:151537400-151558400	Weak transcription	Fetal Kidney	kidney
9	chr1:151538000-151557400	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:151539000-151556400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:151539000-151557000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:151541200-151557000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:151541400-151556400	Strong transcription	Fetal Stomach	stomach
14	chr1:151542000-151557000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:151542600-151557400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:151542800-151556600	Strong transcription	Fetal Intestine Small	intestine
17	chr1:151542800-151556600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:151543800-151556400	Strong transcription	Fetal Intestine Large	intestine
19	chr1:151545200-151556600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:151547400-151556000	Weak transcription	Spleen	Spleen
21	chr1:151547600-151556200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:151547600-151556200	Weak transcription	HUVEC	blood vessel
23	chr1:151548000-151556200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:151548000-151556800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:151548000-151557200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:151548400-151557400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:151548800-151557200	Strong transcription	Brain Germinal Matrix	brain
28	chr1:151548800-151558200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:151549000-151556200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:151550000-151556400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:151550200-151556600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:151550400-151559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:151550800-151557600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:151551000-151557000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:151551200-151556600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:151551800-151556600	Weak transcription	Stomach Mucosa	stomach
37	chr1:151551800-151557800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:151552200-151556000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:151552200-151556200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:151552200-151556800	Strong transcription	Osteobl	bone
41	chr1:151552400-151556000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:151552400-151556200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:151552400-151556200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:151552400-151556200	Strong transcription	A549	lung
45	chr1:151552400-151558200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:151552600-151555800	Strong transcription	HSMM	muscle
47	chr1:151552600-151556400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:151552600-151556400	Weak transcription	Right Ventricle	heart
49	chr1:151552600-151557200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:151552600-151559800	Weak transcription	H9 Cell Line	embryonic stem cell

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