Variant report

Variant	rs11729403
Chromosome Location	chr4:56267182-56267183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:56267004-56267374	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:56267055-56267867	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56266067..56267699-chr4:56271922..56273908,2	MCF-7	breast:
2	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
3	chr4:56211281..56215987-chr4:56257992..56268538,18	K562	blood:
4	chr4:56210761..56214527-chr4:56265668..56271169,8	K562	blood:
5	chr4:56206647..56208292-chr4:56265434..56267347,2	MCF-7	breast:

Variant related genes	Relation type
TMEM165	TF binding region
ENSG00000251111	Chromatin interaction
ENSG00000128039	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10026202	0.92[AMR][1000 genomes]
rs10031345	0.84[AMR][1000 genomes]
rs11722277	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11722415	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11723580	1.00[AFR][1000 genomes]
rs11724300	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11725081	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11725422	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11725439	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11725592	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11725738	0.80[EUR][1000 genomes]
rs11727248	0.80[EUR][1000 genomes]
rs11727642	0.92[AMR][1000 genomes]
rs11729092	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11732078	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11732684	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11733959	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11733966	1.00[AFR][1000 genomes]
rs1522113	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28391333	0.92[AMR][1000 genomes]
rs28409498	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28450557	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28588862	0.84[AMR][1000 genomes]
rs28873832	0.92[AMR][1000 genomes]
rs34897046	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35133040	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35793438	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7356345	0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv3513387	chr4:56265445-56270643	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3513386	chr4:56265495-56269293	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3513388	chr4:56265495-56269293	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv20248	chr4:56266121-56267944	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv594204	chr4:56266973-56268507	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56264200-56267400	Enhancers	Small Intestine	intestine
2	chr4:56264200-56269800	Weak transcription	Spleen	Spleen
3	chr4:56264200-56270200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:56264200-56273000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:56264600-56270000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:56264800-56269800	Weak transcription	Fetal Kidney	kidney
7	chr4:56264800-56282200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:56265000-56273200	Weak transcription	Gastric	stomach
10	chr4:56265400-56273400	Weak transcription	Aorta	Aorta
11	chr4:56265600-56267200	Weak transcription	HepG2	liver
12	chr4:56265600-56268200	Strong transcription	HSMM	muscle
13	chr4:56265600-56269200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:56265600-56269200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:56265600-56269200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:56265600-56269200	Weak transcription	HSMMtube	muscle
17	chr4:56265600-56269800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:56265600-56269800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:56265600-56269800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:56265600-56269800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:56265600-56269800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:56265600-56270200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:56265600-56270200	Weak transcription	Lung	lung
24	chr4:56265600-56270200	Weak transcription	Thymus	Thymus
25	chr4:56265600-56271400	Weak transcription	Psoas Muscle	Psoas
26	chr4:56265600-56271800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:56265600-56272000	Weak transcription	Esophagus	oesophagus
28	chr4:56265600-56272200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:56265600-56273200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:56265600-56273800	Weak transcription	Stomach Mucosa	stomach
31	chr4:56265600-56275600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:56265600-56281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:56265600-56283800	Weak transcription	Fetal Brain Male	brain
34	chr4:56265600-56286000	Weak transcription	Colonic Mucosa	Colon
35	chr4:56265600-56289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:56265800-56267800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:56265800-56267800	Strong transcription	Osteobl	bone
39	chr4:56265800-56268000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:56265800-56269400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:56265800-56271400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:56265800-56271600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:56265800-56271600	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:56265800-56274400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:56265800-56275200	Weak transcription	Fetal Heart	heart
46	chr4:56265800-56281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:56266000-56267600	Genic enhancers	Dnd41	blood
48	chr4:56266000-56268000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:56266000-56268000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr4:56266000-56269200	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links