Variant report

Variant	rs6692451
Chromosome Location	chr1:169846883-169846884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169844705..169847129-chr1:169861263..169863239,3	MCF-7	breast:
2	chr1:169798250..169800377-chr1:169845673..169848267,2	K562	blood:
3	chr1:169845321..169846924-chr1:169848823..169850416,2	K562	blood:
4	chr1:169845717..169848182-chr1:169860925..169862962,2	MCF-7	breast:
5	chr1:169846456..169849390-chr1:169863296..169865489,2	MCF-7	breast:
6	chr1:169846082..169850359-chr1:169859892..169864668,5	K562	blood:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12032210	1.00[CHB][hapmap]
rs12038720	0.82[ASN][1000 genomes]
rs12044905	0.82[ASN][1000 genomes]
rs2273459	0.82[ASN][1000 genomes]
rs3790406	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[ASN][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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6692451	C1orf156	cis	uninvolved skin	skin_eQTL
rs6692451	C1orf156	cis	lymphoblastoid	seeQTL
rs6692451	C1orf156	cis	lesional skin	skin_eQTL
rs6692451	C1orf156	Cis_1M	lymphoblastoid	RTeQTL
rs6692451	METTL18	cis	Heart Left Ventricle	GTEx
rs6692451	METTL18	cis	Esophagus Muscularis	GTEx
rs6692451	C1orf112	cis	cerebellum	SCAN
rs6692451	METTL18	cis	Artery Tibial	GTEx
rs6692451	TIPRL	cis	cerebellum	SCAN
rs6692451	C1orf156	cis	parietal	SCAN
rs6692451	C1orf156	cis	cerebellum	SCAN
rs6692451	METTL18	cis	Esophagus Mucosa	GTEx
rs6692451	METTL18	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
4	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr1:169814800-169848000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:169815200-169848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:169817800-169848600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr1:169818200-169847800	Strong transcription	Adipose Nuclei	Adipose
10	chr1:169819000-169848200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:169819400-169847000	Strong transcription	Liver	Liver
12	chr1:169820400-169847200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:169820600-169847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:169820600-169847800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:169820600-169848400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:169820600-169848600	Strong transcription	Fetal Lung	lung
17	chr1:169826800-169848600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:169831800-169848400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:169833400-169847000	Strong transcription	Left Ventricle	heart
20	chr1:169833800-169860200	Weak transcription	HMEC	breast
21	chr1:169837400-169848000	Strong transcription	Brain Anterior Caudate	brain
22	chr1:169841000-169847200	Strong transcription	Brain Substantia Nigra	brain
23	chr1:169841000-169847400	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr1:169841600-169847000	Strong transcription	Ovary	ovary
25	chr1:169841600-169847200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:169841800-169848200	Strong transcription	Placenta	Placenta
27	chr1:169841800-169848400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:169841800-169848400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:169841800-169848600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:169841800-169848600	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:169842000-169847200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:169842000-169848000	Strong transcription	Thymus	Thymus
33	chr1:169842000-169848400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:169842000-169848400	Strong transcription	Fetal Thymus	thymus
35	chr1:169842000-169848600	Strong transcription	Fetal Intestine Large	intestine
36	chr1:169842200-169847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:169842200-169857400	Weak transcription	Fetal Brain Male	brain
38	chr1:169842400-169847000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:169842400-169847000	Weak transcription	NHLF	lung
40	chr1:169842400-169847800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:169842400-169848400	Strong transcription	Dnd41	blood
42	chr1:169842400-169848800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:169842400-169850800	Weak transcription	Esophagus	oesophagus
44	chr1:169842400-169851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:169842400-169851000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:169842400-169855600	Weak transcription	Brain Angular Gyrus	brain
47	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:169842600-169847800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:169842600-169854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:169843000-169847800	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links