Variant report

Variant	rs11728415
Chromosome Location	chr4:7807196-7807197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7773384..7775813-chr4:7806131..7807839,2	MCF-7	breast:
2	chr4:7806581..7808350-chr4:8014117..8016969,2	MCF-7	breast:
3	chr4:7806783..7809609-chr4:7939273..7941651,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10516189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11723068	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11724590	0.85[CHB][hapmap]
rs11725132	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11725213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11727624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11731614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11731850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11736326	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11736912	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16841112	0.89[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs16841187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16841215	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16841246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2017177	0.84[AMR][1000 genomes]
rs2240053	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs2240054	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs2240055	0.84[AMR][1000 genomes]
rs2269849	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2269878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2276967	0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2285766	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2285767	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2285769	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2285770	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2285771	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs28604598	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4538480	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4689162	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4689165	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4689862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4689863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4997103	0.89[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55677626	0.82[AMR][1000 genomes]
rs55752670	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58790280	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58957020	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67476190	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67725344	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6852934	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs757252	0.84[AMR][1000 genomes]
rs7660919	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7695250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[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	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
7	esv2763337	chr4:7807183-7811303	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
3	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
4	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr4:7798200-7807200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:7800200-7807200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:7800600-7828800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:7801400-7807200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:7801400-7807400	Weak transcription	Right Ventricle	heart
11	chr4:7801800-7807400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:7802000-7807200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:7802000-7807200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:7802000-7807800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:7802200-7819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:7802400-7812400	Weak transcription	Spleen	Spleen
17	chr4:7802600-7807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:7802600-7807400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:7802600-7808000	Weak transcription	Gastric	stomach
20	chr4:7802600-7809600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:7802600-7810400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr4:7802800-7807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:7802800-7807200	Weak transcription	Brain Anterior Caudate	brain
24	chr4:7802800-7807400	Weak transcription	Left Ventricle	heart
25	chr4:7802800-7807600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:7802800-7809400	Weak transcription	Esophagus	oesophagus
27	chr4:7803000-7808000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:7803000-7808600	Weak transcription	Aorta	Aorta
29	chr4:7803000-7812400	Weak transcription	Colonic Mucosa	Colon
30	chr4:7803400-7807400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:7803800-7809200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:7803800-7810200	Enhancers	Fetal Heart	heart
33	chr4:7804000-7829200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:7804200-7808200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:7804200-7808200	Weak transcription	NHEK	skin
36	chr4:7804600-7809400	Genic enhancers	Osteobl	bone
37	chr4:7805000-7807600	Genic enhancers	Fetal Muscle Leg	muscle
38	chr4:7805200-7809600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:7805200-7822600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:7805400-7807200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:7805400-7807600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr4:7805400-7809600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:7805600-7807400	Enhancers	Placenta	Placenta
44	chr4:7805600-7807400	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr4:7805600-7807600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr4:7805600-7809600	Enhancers	Colon Smooth Muscle	Colon
47	chr4:7805600-7809800	Enhancers	Brain Hippocampus Middle	brain
48	chr4:7805600-7810400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr4:7805600-7816400	Genic enhancers	Fetal Stomach	stomach
50	chr4:7805800-7807400	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links