Variant report

Variant	rs4443499
Chromosome Location	chr6:53599583-53599584
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53516373..53518187-chr6:53597538..53600553,4	MCF-7	breast:
2	chr6:53411604..53413462-chr6:53597893..53600161,2	MCF-7	breast:
3	chr6:53595711..53597938-chr6:53598268..53600839,2	MCF-7	breast:
4	chr6:53583394..53584065-chr6:53599288..53600218,2	MCF-7	breast:
5	chr6:53590810..53593190-chr6:53597036..53600341,4	K562	blood:
6	chr6:53598898..53601641-chr6:53603723..53606379,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10456164	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10456671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193312	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12197259	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13191282	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13195168	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13196802	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13206978	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13211007	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13219456	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3000995	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003502	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4302662	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4409173	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4416674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4428502	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4469293	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4479931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4555913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574642	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4715423	1.00[CEU][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458955	0.85[EUR][1000 genomes]
rs6909833	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930030	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930035	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7745277	0.94[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];0.99[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755196	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7755522	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7773640	0.85[CEU][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4443499	C6orf142	cis	cerebellum	SCAN
rs4443499	HMGCLL1	cis	parietal	SCAN
rs4443499	KLHL31	cis	Skin Sun Exposed Lower leg	GTEx
rs4443499	PRIM2	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53591200-53599600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr6:53591200-53599800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:53591600-53599600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:53593000-53599800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:53593600-53599800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:53593600-53600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:53593800-53599800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:53594600-53599600	Weak transcription	Placenta	Placenta
9	chr6:53595000-53599800	Enhancers	Dnd41	blood
10	chr6:53595400-53599800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:53596000-53599600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:53596000-53599600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:53596000-53601600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:53596000-53605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:53597200-53599600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:53597200-53599600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr6:53597200-53599800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:53597200-53604000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:53597400-53599800	Weak transcription	Primary T cells from cord blood	blood
20	chr6:53597400-53599800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:53597400-53600000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:53597800-53599600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:53598400-53601000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:53598400-53601200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:53598400-53601400	Enhancers	Fetal Intestine Small	intestine
26	chr6:53598400-53603000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:53598600-53601400	Enhancers	Fetal Intestine Large	intestine
28	chr6:53599000-53600000	Enhancers	Stomach Mucosa	stomach
29	chr6:53599000-53600400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:53599000-53601000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:53599200-53599600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr6:53599200-53599800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:53599200-53599800	Flanking Active TSS	HUVEC	blood vessel
34	chr6:53599200-53600000	Flanking Active TSS	A549	lung
35	chr6:53599200-53600600	Enhancers	HSMM	muscle
36	chr6:53599200-53601200	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:53599200-53603000	Enhancers	Fetal Heart	heart
38	chr6:53599400-53599600	Enhancers	Rectal Smooth Muscle	rectum
39	chr6:53599400-53599600	Enhancers	HMEC	breast
40	chr6:53599400-53599600	Enhancers	NHEK	skin
41	chr6:53599400-53599800	Enhancers	H9 Cell Line	embryonic stem cell
42	chr6:53599400-53599800	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr6:53599400-53599800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:53599400-53599800	Enhancers	Osteobl	bone
45	chr6:53599400-53600000	Flanking Active TSS	Hela-S3	cervix
46	chr6:53599400-53600000	Flanking Active TSS	NH-A	brain
47	chr6:53599400-53600400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:53599400-53601000	Enhancers	GM12878-XiMat	blood
49	chr6:53599400-53601200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:53599400-53601200	Enhancers	Fetal Thymus	thymus

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