Variant report

Variant	rs1883327
Chromosome Location	chr6:4848934-4848935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4847558..4849642-chr6:4852103..4854411,2	K562	blood:
2	chr6:4848197..4852151-chr6:4852565..4855208,4	MCF-7	breast:
3	chr6:4776573..4778136-chr6:4847031..4849578,2	K562	blood:
4	chr6:4845889..4847519-chr6:4848149..4850482,2	MCF-7	breast:
5	chr6:4840303..4841822-chr6:4847282..4849004,2	MCF-7	breast:
6	chr6:4807875..4808462-chr6:4848723..4849408,2	MCF-7	breast:
7	chr6:4847745..4850576-chr6:4852287..4854812,4	K562	blood:

Variant related genes	Relation type
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1265336	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1771884	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233477	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs233479	0.93[ASW][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs55653939	0.83[ASN][1000 genomes]
rs7763686	0.91[ASN][1000 genomes]
rs808589	0.86[ASN][1000 genomes]
rs808603	0.85[ASN][1000 genomes]
rs808611	0.81[ASN][1000 genomes]
rs808615	0.93[ASW][hapmap];0.87[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs808622	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]

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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1015888	chr6:4787784-4883663	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv966675	chr6:4819733-4855009	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1883327	SERPINB6	cis	cerebellum	SCAN
rs1883327	RIOK1	cis	cerebellum	SCAN
rs1883327	CDYL	cis	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4821200-4853600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:4844600-4859600	Weak transcription	Spleen	Spleen
3	chr6:4844800-4853200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:4844800-4854000	Weak transcription	NHEK	skin
5	chr6:4844800-4856600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:4844800-4863000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:4845000-4849400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:4846000-4849200	Enhancers	Psoas Muscle	Psoas
9	chr6:4846400-4850600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:4846400-4859000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:4846800-4849000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:4847000-4849000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:4847200-4849200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:4847200-4849200	Enhancers	Ovary	ovary
15	chr6:4847400-4849200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr6:4847400-4854000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:4847400-4871000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:4847600-4849200	Enhancers	Brain Substantia Nigra	brain
19	chr6:4847600-4850000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:4847600-4853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:4847600-4853800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:4847600-4854000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:4847600-4854000	Weak transcription	Lung	lung
24	chr6:4847800-4849000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr6:4847800-4849200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr6:4848000-4850000	Enhancers	HUVEC	blood vessel
27	chr6:4848200-4849800	Enhancers	K562	blood
28	chr6:4848400-4849000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:4848400-4849000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr6:4848400-4849200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:4848400-4849600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:4848400-4849800	Enhancers	Rectal Smooth Muscle	rectum
33	chr6:4848400-4849800	Enhancers	Small Intestine	intestine
34	chr6:4848400-4850000	Enhancers	Fetal Heart	heart
35	chr6:4848400-4850600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr6:4848600-4849000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:4848600-4849000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:4848600-4849000	Enhancers	H9 Cell Line	embryonic stem cell
39	chr6:4848600-4849000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr6:4848600-4849000	Active TSS	Aorta	Aorta
41	chr6:4848600-4849000	Enhancers	Left Ventricle	heart
42	chr6:4848600-4849000	Enhancers	Right Atrium	heart
43	chr6:4848600-4849000	Enhancers	Right Ventricle	heart
44	chr6:4848600-4849000	Enhancers	HepG2	liver
45	chr6:4848600-4849000	Enhancers	HSMM	muscle
46	chr6:4848600-4849000	Enhancers	NHLF	lung
47	chr6:4848600-4849200	Enhancers	Brain Anterior Caudate	brain
48	chr6:4848600-4849200	Enhancers	Gastric	stomach
49	chr6:4848600-4849400	Enhancers	Fetal Lung	lung
50	chr6:4848600-4849400	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links