Variant report

Variant	rs28612371
Chromosome Location	chr2:47175158-47175159
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47170300..47176373-chr2:47180929..47185322,6	MCF-7	breast:
2	chr2:47173359..47175767-chr2:47176335..47179186,3	MCF-7	breast:
3	chr2:47174154..47179572-chr2:47181486..47185069,4	MCF-7	breast:
4	chr2:47165446..47170208-chr2:47173646..47177856,9	MCF-7	breast:
5	chr2:47168010..47171387-chr2:47174663..47177261,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272814	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10084332	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10164756	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10165085	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10186980	0.80[EUR][1000 genomes]
rs11897050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13391660	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13398748	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13406024	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13407588	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13409489	0.98[EUR][1000 genomes]
rs13417753	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13424086	0.83[EUR][1000 genomes]
rs13430346	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13430703	0.98[EUR][1000 genomes]
rs17035878	0.83[EUR][1000 genomes]
rs17035912	0.95[EUR][1000 genomes]
rs28405928	0.83[EUR][1000 genomes]
rs28465613	0.80[EUR][1000 genomes]
rs28529158	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28770495	0.83[EUR][1000 genomes]
rs4300885	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4314044	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4583513	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6729569	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6755386	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73926967	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73926970	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73926978	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73926980	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73926983	0.95[EUR][1000 genomes]
rs73926986	0.95[EUR][1000 genomes]
rs73926988	0.95[EUR][1000 genomes]
rs73926990	0.87[AFR][1000 genomes]
rs73926991	0.82[AFR][1000 genomes]
rs7577816	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7603884	0.95[EUR][1000 genomes]
rs9973769	0.86[AMR][1000 genomes];0.95[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS 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 miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169400-47178800	Weak transcription	Ovary	ovary
2	chr2:47169400-47179000	Weak transcription	Gastric	stomach
3	chr2:47169600-47177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:47169600-47177600	Weak transcription	Left Ventricle	heart
5	chr2:47169600-47178800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:47169600-47183600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:47169800-47177600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:47169800-47177600	Weak transcription	Fetal Lung	lung
9	chr2:47169800-47178200	Weak transcription	Fetal Brain Female	brain
10	chr2:47169800-47182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:47169800-47182200	Weak transcription	Right Ventricle	heart
12	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
13	chr2:47170000-47177000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:47170000-47177400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:47170000-47177600	Weak transcription	Esophagus	oesophagus
16	chr2:47170000-47177800	Weak transcription	Liver	Liver
17	chr2:47170000-47177800	Weak transcription	NH-A	brain
18	chr2:47170000-47178800	Weak transcription	HSMMtube	muscle
19	chr2:47170000-47181600	Weak transcription	HUVEC	blood vessel
20	chr2:47170000-47182200	Weak transcription	Psoas Muscle	Psoas
21	chr2:47170200-47177600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:47170200-47181400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:47170400-47177400	Weak transcription	Fetal Intestine Large	intestine
24	chr2:47170600-47178800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:47170800-47176000	Strong transcription	Fetal Stomach	stomach
26	chr2:47170800-47177600	Weak transcription	K562	blood
27	chr2:47170800-47178200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:47170800-47184000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:47171000-47176200	Enhancers	Primary hematopoietic stem cells	blood
30	chr2:47171000-47177600	Weak transcription	Aorta	Aorta
31	chr2:47171000-47177600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:47171000-47178200	Weak transcription	Colonic Mucosa	Colon
33	chr2:47171000-47178200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:47171000-47178400	Weak transcription	Stomach Mucosa	stomach
35	chr2:47171000-47182600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:47171200-47178800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:47171200-47178800	Weak transcription	NHDF-Ad	bronchial
38	chr2:47171200-47179400	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr2:47171200-47182400	Weak transcription	Small Intestine	intestine
40	chr2:47171400-47177200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:47171400-47177400	Weak transcription	Brain Angular Gyrus	brain
42	chr2:47171400-47177600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:47171400-47177600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:47171400-47179800	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:47171400-47182000	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:47171600-47175400	Strong transcription	NHLF	lung
47	chr2:47171600-47176000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:47171600-47177200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:47171600-47177400	Weak transcription	Brain Anterior Caudate	brain
50	chr2:47171800-47176200	Enhancers	Primary T helper cells fromperipheralblood	blood

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