Variant report

Variant	rs1887340
Chromosome Location	chr6:33730095-33730096
allele	C/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:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33538562..33539178-chr6:33730064..33730663,2	K562	blood:
2	chr6:33729702..33730489-chr6:33784415..33785270,3	MCF-7	breast:
3	chr6:33674794..33680843-chr6:33726905..33731016,6	MCF-7	breast:
4	chr6:33681908..33683361-chr6:33729732..33730584,6	MCF-7	breast:
5	chr6:33679209..33680073-chr6:33729725..33730535,3	MCF-7	breast:
6	chr6:33684529..33686540-chr6:33729478..33731636,2	MCF-7	breast:
7	chr6:33727358..33730164-chr6:33732846..33736236,4	K562	blood:
8	chr6:33682318..33683476-chr6:33729673..33730365,3	MCF-7	breast:
9	chr6:33553147..33553827-chr6:33730088..33730602,2	K562	blood:
10	chr6:33711824..33712826-chr6:33729422..33730557,4	K562	blood:
11	chr6:33728564..33732066-chr6:33733725..33737558,5	MCF-7	breast:
12	chr6:33681000..33683302-chr6:33729065..33730662,2	MCF-7	breast:
13	chr6:33679206..33680031-chr6:33729674..33730625,9	MCF-7	breast:
14	chr6:33557128..33558070-chr6:33729670..33730677,6	K562	blood:
15	chr6:33708694..33710403-chr6:33728367..33730684,2	MCF-7	breast:
16	chr6:33710878..33712572-chr6:33728483..33730415,2	K562	blood:
17	chr6:33729937..33730541-chr6:34122442..34123101,2	K562	blood:
18	chr6:33717929..33721430-chr6:33728075..33731260,3	MCF-7	breast:
19	chr6:33679162..33680218-chr6:33729935..33730915,4	K562	blood:
20	chr6:33729337..33731009-chr6:33738048..33739817,2	MCF-7	breast:
21	chr6:33684753..33687394-chr6:33728535..33731247,2	MCF-7	breast:
22	chr6:33711863..33712830-chr6:33729590..33730729,7	MCF-7	breast:
23	chr6:33721254..33721988-chr6:33729704..33730219,2	K562	blood:
24	chr6:33712090..33712713-chr6:33729680..33730317,2	MCF-7	breast:
25	chr6:33678876..33680749-chr6:33729962..33732135,3	K562	blood:
26	chr6:33710780..33712378-chr6:33728766..33730415,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1075379	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs11753083	0.94[EUR][1000 genomes]
rs11754690	1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs11755593	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11757524	0.94[EUR][1000 genomes]
rs11758463	0.93[EUR][1000 genomes]
rs12524768	0.93[EUR][1000 genomes]
rs12524835	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2281819	0.86[EUR][1000 genomes]
rs2281820	0.90[CHB][hapmap]
rs2395400	0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs2894342	0.86[EUR][1000 genomes]
rs3763253	0.86[EUR][1000 genomes]
rs3828783	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4711345	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs4711346	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55775340	0.95[EUR][1000 genomes]
rs59137082	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61394483	0.94[EUR][1000 genomes]
rs61662306	0.94[EUR][1000 genomes]
rs6910736	0.89[EUR][1000 genomes]
rs6921487	0.93[EUR][1000 genomes]
rs6930201	0.94[EUR][1000 genomes]
rs6933174	0.94[EUR][1000 genomes]
rs6933568	0.93[EUR][1000 genomes]
rs6933607	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs6940353	0.94[EUR][1000 genomes]
rs72880511	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73412140	0.94[EUR][1000 genomes]
rs73746509	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs747692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs747693	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs751096	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs755495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7755323	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs943461	0.94[EUR][1000 genomes]
rs943462	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs943466	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33715200-33737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:33720200-33730600	Weak transcription	Spleen	Spleen
3	chr6:33723400-33736600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:33724000-33730200	Enhancers	Stomach Mucosa	stomach
5	chr6:33726000-33731000	Enhancers	Fetal Stomach	stomach
6	chr6:33726200-33731000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:33726200-33731400	Enhancers	Fetal Lung	lung
8	chr6:33726400-33738200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:33727000-33730800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:33728000-33730200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:33728000-33730800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:33728000-33731400	Enhancers	Fetal Muscle Leg	muscle
13	chr6:33728000-33732000	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:33728200-33730400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:33728600-33730600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:33728800-33730800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:33728800-33731600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr6:33728800-33731600	Enhancers	Right Ventricle	heart
19	chr6:33729000-33730200	Enhancers	Colonic Mucosa	Colon
20	chr6:33729000-33730200	Genic enhancers	Right Atrium	heart
21	chr6:33729000-33730800	Enhancers	Fetal Intestine Small	intestine
22	chr6:33729000-33736200	Weak transcription	HSMM	muscle
23	chr6:33729200-33730200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:33729200-33730200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:33729200-33730200	Enhancers	Duodenum Mucosa	Duodenum
26	chr6:33729200-33730200	Enhancers	Pancreas	Pancrea
27	chr6:33729200-33732000	Enhancers	Placenta	Placenta
28	chr6:33729400-33730200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:33729400-33730200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:33729400-33730200	Enhancers	Esophagus	oesophagus
31	chr6:33729400-33730200	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr6:33729400-33730800	Enhancers	Brain Substantia Nigra	brain
33	chr6:33729400-33730800	Enhancers	Fetal Intestine Large	intestine
34	chr6:33729600-33730200	Enhancers	Adipose Nuclei	Adipose
35	chr6:33729600-33730200	Enhancers	Brain Hippocampus Middle	brain
36	chr6:33729600-33730200	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr6:33729600-33730200	Flanking Active TSS	HepG2	liver
38	chr6:33729600-33730600	Enhancers	Brain Cingulate Gyrus	brain
39	chr6:33729600-33730800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr6:33729800-33730200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:33729800-33730200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr6:33729800-33730200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:33729800-33730200	Enhancers	HMEC	breast
44	chr6:33729800-33730600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:33729800-33730600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr6:33729800-33734800	Weak transcription	HSMMtube	muscle
47	chr6:33730000-33730200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:33730000-33730200	Enhancers	Gastric	stomach
49	chr6:33730000-33730400	Enhancers	Colon Smooth Muscle	Colon
50	chr6:33730000-33730600	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links