Variant report

Variant	rs4538169
Chromosome Location	chr2:173163001-173163002
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	chr2:173156581..173161480-chr2:173162847..173166156,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA6-1	chr2:173162942-173163071	XLOC_001757
2	lnc-ITGA6-2	chr2:173162925-173163071	NONHSAT075495
3	lnc-ITGA6-1	chr2:173162904-173163071	XLOC_001757

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10930540	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930541	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10930542	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930545	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930547	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11674489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11674629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11674681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11677934	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11677943	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11685584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12624040	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384490	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429441	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4438453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447582	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4450575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4594405	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4619572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972477	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4972774	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972775	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55893326	0.85[EUR][1000 genomes]
rs56239652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57101510	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7425702	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[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	nsv3034	chr2:173160295-173200113	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173151400-173168000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173159200-173164400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:173159200-173164600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:173159400-173164200	Weak transcription	HMEC	breast
5	chr2:173160600-173163200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
6	chr2:173161000-173163200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
7	chr2:173161200-173172600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:173161400-173172200	Weak transcription	Right Atrium	heart
9	chr2:173161600-173165800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:173161800-173164400	Weak transcription	NHEK	skin
11	chr2:173162200-173163600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:173162200-173164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:173162200-173164800	Enhancers	HSMMtube	muscle
14	chr2:173162400-173164200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:173162400-173172600	Weak transcription	Fetal Thymus	thymus
16	chr2:173162600-173164200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:173162600-173164200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:173162600-173164200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:173162800-173163200	Weak transcription	Pancreas	Pancrea
20	chr2:173162800-173164600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:173162800-173165000	Enhancers	Fetal Muscle Leg	muscle

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