Variant report

Variant	rs1985899
Chromosome Location	chr6:106552243-106552244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:106549886..106552780-chr6:106576798..106578575,2	MCF-7	breast:
2	chr6:106550794..106552365-chr6:106553055..106555090,2	MCF-7	breast:
3	chr6:106551914..106553458-chr6:106553529..106555381,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1010273	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12175062	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4946722	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4946724	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4946725	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373832	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1832544	chr6:106539914-106642993	Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1985899	PRDM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106546600-106559000	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:106546800-106552800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:106546800-106560200	Weak transcription	HSMM	muscle
4	chr6:106546800-106567000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:106547200-106562600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:106547400-106552800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:106547400-106552800	Weak transcription	Placenta	Placenta
8	chr6:106547400-106553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:106547400-106557200	Strong transcription	Fetal Intestine Large	intestine
10	chr6:106547400-106558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:106547400-106560200	Weak transcription	NH-A	brain
12	chr6:106547600-106556400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:106547800-106552600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:106548000-106552800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
15	chr6:106548000-106553200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:106548000-106556600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:106548400-106561800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:106549200-106552800	Weak transcription	A549	lung
19	chr6:106549600-106554800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:106550000-106552600	Weak transcription	Hela-S3	cervix
21	chr6:106550800-106552600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr6:106550800-106556400	Strong transcription	Fetal Intestine Small	intestine
23	chr6:106551000-106555400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:106551400-106552400	Weak transcription	Small Intestine	intestine
25	chr6:106551400-106555400	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr6:106551600-106552400	Weak transcription	NHDF-Ad	bronchial
27	chr6:106551600-106553000	Weak transcription	Ovary	ovary
28	chr6:106551600-106555200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:106551600-106559200	Weak transcription	Brain Anterior Caudate	brain
30	chr6:106551600-106560400	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:106551600-106563800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:106551800-106552400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:106551800-106552400	Weak transcription	Spleen	Spleen
34	chr6:106551800-106552600	Enhancers	Primary T cells from cord blood	blood
35	chr6:106551800-106552800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:106551800-106552800	Weak transcription	Gastric	stomach
37	chr6:106551800-106553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:106551800-106553000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:106551800-106553000	Weak transcription	Left Ventricle	heart
40	chr6:106551800-106553000	Weak transcription	Lung	lung
41	chr6:106551800-106553200	Weak transcription	Pancreas	Pancrea
42	chr6:106551800-106553800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:106551800-106553800	Weak transcription	Osteobl	bone
44	chr6:106551800-106555000	Weak transcription	K562	blood
45	chr6:106551800-106556200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:106551800-106556400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:106551800-106556400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:106551800-106556400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:106551800-106557800	Weak transcription	Stomach Mucosa	stomach
50	chr6:106551800-106563000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links