Variant report

Variant	rs12029637
Chromosome Location	chr1:94334891-94334892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94332079..94335914-chr1:94341026..94344306,4	K562	blood:
2	chr1:94333834..94335597-chr1:94338840..94340897,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067334	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1051394	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165021	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165022	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165023	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165025	0.89[ASN][1000 genomes]
rs11165026	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12029548	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029670	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12041975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12758972	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2092698	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2092699	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2103784	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2143992	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273165	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273166	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391321	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789459	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3789460	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847191	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847193	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847263	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847264	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6664876	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6666633	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6667991	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681169	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6681265	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6684054	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697189	0.89[ASN][1000 genomes]
rs7364663	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7513489	0.88[ASN][1000 genomes]
rs7513786	0.91[ASN][1000 genomes]
rs7514828	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7517632	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518940	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7555136	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556047	0.85[ASN][1000 genomes]
rs7556107	0.87[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	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12029637	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs12029637	RP11-488P3.1	cis	lung	GTEx
rs12029637	RP11-488P3.1	cis	Thyroid	GTEx
rs12029637	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12029637	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs12029637	DNTTIP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94329800-94335200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:94330000-94337000	Weak transcription	Psoas Muscle	Psoas
5	chr1:94330000-94338800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:94330600-94335200	Weak transcription	NHLF	lung
7	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:94330800-94336800	Weak transcription	Spleen	Spleen
9	chr1:94331000-94339000	Weak transcription	Pancreas	Pancrea
10	chr1:94331400-94335200	Weak transcription	Colonic Mucosa	Colon
11	chr1:94331600-94336600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:94331600-94336800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:94332400-94342000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:94332600-94336200	Weak transcription	Right Ventricle	heart
15	chr1:94332600-94336800	Weak transcription	Lung	lung
16	chr1:94332800-94337000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:94332800-94337000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:94332800-94339600	Weak transcription	Stomach Mucosa	stomach
19	chr1:94332800-94340800	Strong transcription	Left Ventricle	heart
20	chr1:94332800-94341400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:94332800-94341600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:94332800-94341600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:94332800-94341800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:94332800-94341800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:94332800-94341800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:94332800-94343200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:94332800-94343200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:94333000-94336800	Weak transcription	Esophagus	oesophagus
29	chr1:94333000-94337000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:94333000-94341600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:94333000-94342000	Strong transcription	Fetal Brain Female	brain
32	chr1:94333200-94341600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:94333200-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:94333200-94343200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:94333400-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:94333600-94335200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:94333600-94341800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:94333800-94341200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:94333800-94341600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:94333800-94343000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:94334000-94340800	Strong transcription	Brain Anterior Caudate	brain
42	chr1:94334000-94341200	Strong transcription	Primary T cells from cord blood	blood
43	chr1:94334000-94341200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr1:94334000-94341600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:94334000-94341600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:94334000-94341600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:94334000-94341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:94334000-94341800	Strong transcription	Fetal Kidney	kidney
49	chr1:94334000-94341800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:94334000-94342000	Strong transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links