Variant report

Variant	rs7546215
Chromosome Location	chr1:165656104-165656105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165654992..165657269-chr1:165796152..165797744,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143183	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10753688	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs10753689	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10800132	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10800133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918242	0.91[ASN][1000 genomes]
rs10918245	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918251	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10918252	0.86[ASN][1000 genomes]
rs12021795	0.82[ASN][1000 genomes]
rs12033254	0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs12036561	0.91[ASN][1000 genomes]
rs12037790	0.88[ASN][1000 genomes]
rs12084748	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12409168	0.88[ASN][1000 genomes]
rs12567331	0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12728137	0.88[ASN][1000 genomes]
rs17482717	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3845536	0.91[ASN][1000 genomes]
rs4307543	0.91[ASN][1000 genomes]
rs4576644	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4578194	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4646885	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4657463	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4657466	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71628390	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7541817	0.91[ASN][1000 genomes]
rs7546322	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7546215	ENSG00000143149	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165606200-165659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165638000-165666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:165638600-165665400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:165639200-165659800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:165644800-165658800	Strong transcription	HSMM	muscle
6	chr1:165645000-165660200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:165645800-165657400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:165647800-165658400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:165650000-165666800	Weak transcription	Colonic Mucosa	Colon
10	chr1:165651600-165659600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:165651600-165665400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:165651600-165667200	Weak transcription	Gastric	stomach
13	chr1:165651800-165665200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:165651800-165665200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:165651800-165665400	Weak transcription	Small Intestine	intestine
16	chr1:165652000-165664000	Weak transcription	Fetal Brain Male	brain
17	chr1:165652200-165657000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:165652200-165657400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:165652200-165665400	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:165652200-165665800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:165652200-165666000	Weak transcription	Fetal Kidney	kidney
22	chr1:165652200-165666800	Weak transcription	Lung	lung
23	chr1:165652400-165656400	Weak transcription	Fetal Brain Female	brain
24	chr1:165652400-165657200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:165652400-165657200	Weak transcription	HepG2	liver
26	chr1:165652400-165657400	Weak transcription	HUVEC	blood vessel
27	chr1:165652400-165658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:165652400-165659200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:165652400-165659400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:165652400-165659600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:165652400-165659600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:165652400-165659600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:165652400-165659600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:165652400-165659800	Weak transcription	Brain Angular Gyrus	brain
35	chr1:165652400-165665200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:165652400-165665400	Weak transcription	HMEC	breast
37	chr1:165652400-165665400	Weak transcription	NH-A	brain
38	chr1:165652400-165665800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:165652400-165665800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:165652400-165665800	Weak transcription	HSMMtube	muscle
41	chr1:165652400-165666800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:165652400-165666800	Weak transcription	Esophagus	oesophagus
43	chr1:165652400-165667000	Weak transcription	Pancreas	Pancrea
44	chr1:165652400-165667000	Weak transcription	Spleen	Spleen
45	chr1:165652600-165657600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:165652600-165666000	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:165652800-165656400	Weak transcription	Fetal Intestine Large	intestine
48	chr1:165652800-165657400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:165652800-165657800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:165652800-165657800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links