Variant report

Variant	rs2272346
Chromosome Location	chr7:99688822-99688823
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99687387..99689514-chr7:99773501..99775690,2	MCF-7	breast:
2	chr7:99686910..99689525-chr7:99745153..99746949,2	MCF-7	breast:
3	chr16:89785100..89787969-chr7:99688023..99690867,2	MCF-7	breast:
4	chr7:99688297..99690647-chr7:99759308..99762141,2	K562	blood:
5	chr7:99688501..99690139-chr7:99755819..99757970,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213420	Chromatin interaction
ENSG00000075399	Chromatin interaction
ENSG00000188186	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000158805	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1130958	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13228844	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17447058	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17447273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.91[ASN][1000 genomes]
rs2307355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525557	1.00[MEX][hapmap];0.83[TSI][hapmap]
rs41280962	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4134891	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4134911	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4134914	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4134925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4134927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4319008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960542	1.00[CHB][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2272346	PCOLCE	cis	Nerve Tibial	GTEx
rs2272346	PCOLCE-AS1	cis	Nerve Tibial	GTEx
rs2272346	MBLAC1	cis	lymphoblastoid	seeQTL
rs2272346	BUD31	cis	lymphoblastoid	GTEx
rs2272346	COPS6	Cis_1M	lymphoblastoid	RTeQTL
rs2272346	COPS6	cis	lymphoblastoid	seeQTL
rs2272346	MBLAC1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99685800-99689800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:99687200-99690400	Weak transcription	Small Intestine	intestine
3	chr7:99687200-99693000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:99687400-99691200	Weak transcription	Psoas Muscle	Psoas
5	chr7:99687400-99697200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:99687600-99689000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:99687600-99689400	Genic enhancers	HUVEC	blood vessel
8	chr7:99687600-99690200	Strong transcription	Stomach Smooth Muscle	stomach
9	chr7:99687600-99690600	Weak transcription	Stomach Mucosa	stomach
10	chr7:99687600-99696000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr7:99687600-99696600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:99687600-99696800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:99687800-99689000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:99687800-99689000	Genic enhancers	Dnd41	blood
15	chr7:99687800-99689200	Genic enhancers	GM12878-XiMat	blood
16	chr7:99687800-99689200	Genic enhancers	K562	blood
17	chr7:99687800-99689400	Genic enhancers	HSMM	muscle
18	chr7:99687800-99689600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:99687800-99691000	Strong transcription	Fetal Muscle Leg	muscle
20	chr7:99687800-99691200	Strong transcription	Fetal Stomach	stomach
21	chr7:99687800-99691800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:99687800-99692000	Genic enhancers	NH-A	brain
23	chr7:99687800-99696000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:99687800-99696600	Strong transcription	Fetal Intestine Small	intestine
25	chr7:99688000-99689000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr7:99688000-99689200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:99688000-99689600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:99688000-99689600	Strong transcription	Adipose Nuclei	Adipose
29	chr7:99688000-99689800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:99688000-99690000	Strong transcription	Fetal Heart	heart
31	chr7:99688000-99690400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr7:99688000-99690800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:99688000-99690800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:99688000-99690800	Strong transcription	Placenta	Placenta
35	chr7:99688000-99690800	Strong transcription	Lung	lung
36	chr7:99688000-99691000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr7:99688000-99691000	Strong transcription	Rectal Smooth Muscle	rectum
38	chr7:99688000-99691200	Strong transcription	Liver	Liver
39	chr7:99688000-99691200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr7:99688000-99691200	Strong transcription	Right Ventricle	heart
41	chr7:99688000-99691200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:99688000-99693000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr7:99688000-99695400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr7:99688000-99695600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:99688000-99695800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:99688000-99696000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr7:99688000-99696200	Strong transcription	Fetal Intestine Large	intestine
48	chr7:99688000-99696400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr7:99688000-99696400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:99688000-99696400	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links