Variant report

Variant	rs11973
Chromosome Location	chr1:153507105-153507106
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153506466..153507372-chr15:22833387..22834013,2	Hela-S3	cervix:
2	chr1:153505949..153508623-chr1:153516119..153518362,2	K562	blood:
3	chr1:153505870..153508233-chr1:153598440..153600666,2	MCF-7	breast:
4	chr1:153506426..153507317-chr11:64863456..64864140,2	Hela-S3	cervix:
5	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
6	chr1:153505342..153508148-chr1:153641864..153643367,2	MCF-7	breast:
7	chr1:153504382..153507280-chr1:153522086..153523762,2	K562	blood:
8	chr1:153506953..153507640-chr18:9614188..9615055,2	Hela-S3	cervix:
9	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
10	chr1:153506244..153507175-chr19:55895900..55896430,2	Hela-S3	cervix:
11	chr1:153504329..153507150-chr1:153606463..153608211,3	MCF-7	breast:
12	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
13	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
14	chr1:153506299..153508188-chr1:153578857..153582741,3	K562	blood:
15	chr1:153506556..153507277-chr12:113659217..113659722,2	HCT-116	colon:
16	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
17	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:
18	chr1:153505889..153508485-chr1:153582874..153585873,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143621	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000186815	Chromatin interaction
ENSG00000154845	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000153575	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000160679	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11488667	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835357	1.00[EUR][1000 genomes]
rs16835362	1.00[EUR][1000 genomes]
rs16835371	1.00[EUR][1000 genomes]
rs16835373	1.00[EUR][1000 genomes]
rs16835375	1.00[EUR][1000 genomes]
rs16835379	1.00[EUR][1000 genomes]
rs16835389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835409	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835417	1.00[EUR][1000 genomes]
rs2104500	1.00[EUR][1000 genomes]
rs2230870	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28373144	1.00[EUR][1000 genomes]
rs28407716	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28442251	1.00[EUR][1000 genomes]
rs28451322	1.00[EUR][1000 genomes]
rs28456342	1.00[EUR][1000 genomes]
rs28485860	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28510499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28578863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587171	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28605603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28634320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28645589	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648662	1.00[EUR][1000 genomes]
rs28690872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28694652	1.00[EUR][1000 genomes]
rs28709866	1.00[EUR][1000 genomes]
rs28784102	1.00[EUR][1000 genomes]
rs3014827	1.00[EUR][1000 genomes]
rs3856025	1.00[EUR][1000 genomes]
rs56140059	1.00[EUR][1000 genomes]
rs56255753	1.00[EUR][1000 genomes]
rs56401460	1.00[EUR][1000 genomes]
rs58529054	1.00[EUR][1000 genomes]
rs59209384	1.00[EUR][1000 genomes]
rs59617976	1.00[EUR][1000 genomes]
rs60219287	1.00[EUR][1000 genomes]
rs60460123	1.00[EUR][1000 genomes]
rs61038462	1.00[EUR][1000 genomes]
rs61131911	1.00[EUR][1000 genomes]
rs61148582	1.00[EUR][1000 genomes]
rs73009954	1.00[EUR][1000 genomes]
rs73011738	1.00[EUR][1000 genomes]
rs73020460	1.00[EUR][1000 genomes]
rs73020461	1.00[EUR][1000 genomes]
rs73020464	1.00[EUR][1000 genomes]
rs73020467	1.00[EUR][1000 genomes]
rs73020468	1.00[EUR][1000 genomes]
rs73020471	1.00[EUR][1000 genomes]
rs73020473	1.00[EUR][1000 genomes]
rs73020474	1.00[EUR][1000 genomes]
rs73020478	1.00[EUR][1000 genomes]
rs73020479	1.00[EUR][1000 genomes]
rs73020496	1.00[EUR][1000 genomes]
rs73020497	1.00[EUR][1000 genomes]
rs73024502	1.00[EUR][1000 genomes]
rs73026308	1.00[EUR][1000 genomes]
rs730347	1.00[EUR][1000 genomes]
rs74115477	1.00[EUR][1000 genomes]
rs74115478	1.00[EUR][1000 genomes]
rs74115489	1.00[EUR][1000 genomes]
rs746425	1.00[EUR][1000 genomes]
rs7518794	1.00[EUR][1000 genomes]
rs7528738	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7543851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153503400-153507200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:153503800-153507400	Enhancers	Small Intestine	intestine
3	chr1:153504000-153507600	Enhancers	Fetal Thymus	thymus
4	chr1:153504200-153507600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:153504800-153507200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
6	chr1:153504800-153507200	Enhancers	Spleen	Spleen
7	chr1:153504800-153507800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:153504800-153507800	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr1:153504800-153508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:153505000-153507400	Enhancers	Liver	Liver
11	chr1:153505400-153507400	Enhancers	Pancreas	Pancrea
12	chr1:153505400-153507600	Enhancers	Fetal Lung	lung
13	chr1:153505400-153507600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr1:153505400-153507800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:153505400-153507800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:153505400-153507800	Flanking Active TSS	HUVEC	blood vessel
17	chr1:153505400-153508000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr1:153505400-153508000	Enhancers	Fetal Heart	heart
19	chr1:153505400-153508200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:153505400-153508200	Flanking Active TSS	Colonic Mucosa	Colon
21	chr1:153505400-153508400	Flanking Active TSS	NH-A	brain
22	chr1:153505600-153508000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:153505600-153508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:153505800-153508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:153505800-153508400	Flanking Active TSS	Osteobl	bone
26	chr1:153505800-153509200	Active TSS	Aorta	Aorta
27	chr1:153505800-153509400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr1:153506000-153507200	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
29	chr1:153506000-153507400	Enhancers	Gastric	stomach
30	chr1:153506000-153507800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:153506000-153507800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
32	chr1:153506000-153508000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr1:153506000-153508000	Transcr. at gene 5' and 3'	NHLF	lung
34	chr1:153506000-153508200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
35	chr1:153506000-153508400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
36	chr1:153506200-153507400	Enhancers	Psoas Muscle	Psoas
37	chr1:153506200-153507600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
38	chr1:153506200-153507600	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
39	chr1:153506200-153507600	Transcr. at gene 5' and 3'	A549	lung
40	chr1:153506200-153508400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
41	chr1:153506400-153507400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
42	chr1:153506400-153507400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:153506400-153507400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:153506400-153507400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:153506400-153507400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:153506400-153507600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:153506400-153507600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
48	chr1:153506400-153507600	Weak transcription	Brain Germinal Matrix	brain
49	chr1:153506400-153507600	Transcr. at gene 5' and 3'	Esophagus	oesophagus
50	chr1:153506400-153507600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links