Variant report

Variant	rs6899862
Chromosome Location	chr6:30619884-30619885
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30619793-30620454	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:30619714-30620834	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr6:30618623-30620112	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr6:30619486-30619943	K562	blood:	n/a	n/a
5	POLR2A	chr6:30619442-30620668	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr6:30619246-30620771	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:30619438-30620868	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:30619627-30619944	K562	blood:	n/a	n/a
9	POLR2A	chr6:30619727-30620089	K562	blood:	n/a	n/a
10	POLR2A	chr6:30619857-30620800	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30619664..30622989-chr6:30637917..30640970,3	MCF-7	breast:
2	chr6:30580789..30587552-chr6:30608606..30620072,66	K562	blood:
3	chr6:30618609..30620115-chr6:30628547..30631052,2	MCF-7	breast:
4	chr6:30618982..30621616-chr6:30685641..30687439,2	K562	blood:

No data

Variant related genes	Relation type
C6orf136	TF binding region
ENSG00000137337	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204560	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs16867845	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17189120	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17189134	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17189155	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17195411	0.94[ASN][1000 genomes]
rs17195474	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17195488	0.94[ASN][1000 genomes]
rs17195516	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2106069	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239514	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239515	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239516	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2267638	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2267640	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2302347	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2394387	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2394388	0.94[ASN][1000 genomes]
rs2394389	0.94[ASN][1000 genomes]
rs3815101	0.94[ASN][1000 genomes]
rs4148247	0.94[ASN][1000 genomes]
rs58423891	0.89[ASN][1000 genomes]
rs59272830	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59607822	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59913575	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60081418	0.94[ASN][1000 genomes]
rs60120766	0.81[ASN][1000 genomes]
rs60399658	0.83[ASN][1000 genomes]
rs61733213	0.83[ASN][1000 genomes]
rs6457246	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6457247	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6457248	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6457249	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6899769	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6901251	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6911174	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6917434	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6917935	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6934466	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7742291	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7742650	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7742754	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7749109	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7749807	0.94[ASN][1000 genomes]
rs7749978	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7767002	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7773711	0.83[ASN][1000 genomes]
rs9262120	0.94[ASN][1000 genomes]
rs9468812	0.83[ASN][1000 genomes]
rs9671	0.87[EUR][1000 genomes];0.94[ASN][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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription 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	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30616000-30627000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:30616200-30620200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:30616200-30620200	Weak transcription	HSMM	muscle
4	chr6:30616200-30620200	Weak transcription	NHLF	lung
5	chr6:30616200-30620600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:30616200-30620600	Weak transcription	GM12878-XiMat	blood
7	chr6:30616200-30621000	Weak transcription	HUVEC	blood vessel
8	chr6:30616200-30622000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:30616200-30622400	Weak transcription	NHDF-Ad	bronchial
10	chr6:30616200-30627600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:30616200-30627600	Weak transcription	Fetal Brain Male	brain
12	chr6:30616200-30630800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:30616200-30639800	Weak transcription	Right Atrium	heart
14	chr6:30616400-30620200	Weak transcription	Hela-S3	cervix
15	chr6:30616400-30620600	Weak transcription	Fetal Kidney	kidney
16	chr6:30616400-30622400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:30617000-30620200	Weak transcription	Fetal Heart	heart
18	chr6:30617200-30621000	Strong transcription	A549	lung
19	chr6:30617200-30628400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr6:30617200-30636200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:30617200-30636400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:30617200-30636600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:30617200-30638600	Strong transcription	Fetal Stomach	stomach
24	chr6:30617200-30638600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:30617200-30638800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:30617200-30638800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:30617200-30639000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:30617200-30639000	Strong transcription	Fetal Intestine Small	intestine
29	chr6:30617200-30639000	Strong transcription	Thymus	Thymus
30	chr6:30617400-30623000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:30617400-30623400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:30617400-30630800	Strong transcription	Right Ventricle	heart
33	chr6:30617400-30634200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:30617400-30636000	Strong transcription	Colon Smooth Muscle	Colon
35	chr6:30617400-30636400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:30617400-30636600	Strong transcription	Rectal Smooth Muscle	rectum
37	chr6:30617400-30638400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr6:30617400-30638600	Strong transcription	Fetal Thymus	thymus
39	chr6:30617400-30638800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:30617400-30639000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr6:30617400-30639000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:30617400-30639200	Strong transcription	Fetal Muscle Leg	muscle
43	chr6:30617600-30622800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:30617600-30622800	Strong transcription	Liver	Liver
45	chr6:30617600-30633800	Strong transcription	Left Ventricle	heart
46	chr6:30617600-30634200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:30617600-30638800	Strong transcription	Primary T cells from cord blood	blood
48	chr6:30617600-30638800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:30617600-30639000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr6:30617600-30639000	Strong transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links