Variant report

Variant	rs2289258
Chromosome Location	chr12:104173880-104173881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104171358..104174943-chr12:104233480..104236232,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1057892	0.84[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11829459	0.80[ASN][1000 genomes]
rs12229599	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12422418	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12422615	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12422701	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12423476	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs12423889	0.81[EUR][1000 genomes]
rs12423912	0.90[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12423929	0.81[AMR][1000 genomes]
rs12423994	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12424929	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12424984	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12425283	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1437505	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs1550207	0.83[EUR][1000 genomes]
rs1550208	0.83[EUR][1000 genomes]
rs17034464	0.81[AMR][1000 genomes]
rs17034524	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs17034527	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs17034593	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17034620	0.83[EUR][1000 genomes]
rs17034625	0.82[EUR][1000 genomes]
rs17034635	1.00[YRI][hapmap]
rs17034637	0.83[EUR][1000 genomes]
rs17034639	0.83[EUR][1000 genomes]
rs17034640	0.83[EUR][1000 genomes]
rs17034642	0.83[EUR][1000 genomes]
rs17034645	0.83[EUR][1000 genomes]
rs17034648	0.83[EUR][1000 genomes]
rs17034650	0.83[EUR][1000 genomes]
rs17034662	0.83[EUR][1000 genomes]
rs17794246	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3751196	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3812802	0.89[EUR][1000 genomes]
rs55724382	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55736751	0.80[EUR][1000 genomes]
rs55810720	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55932227	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55949441	0.83[EUR][1000 genomes]
rs55987022	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56123042	0.83[EUR][1000 genomes]
rs56143748	0.83[EUR][1000 genomes]
rs56147174	0.82[EUR][1000 genomes]
rs56255894	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56314567	0.83[EUR][1000 genomes]
rs56403068	0.81[EUR][1000 genomes]
rs57412476	0.84[AFR][1000 genomes]
rs59651914	0.83[EUR][1000 genomes]
rs59716163	0.81[EUR][1000 genomes]
rs60378307	0.81[EUR][1000 genomes]
rs61512578	0.83[EUR][1000 genomes]
rs61748068	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7295408	0.89[EUR][1000 genomes]
rs7314150	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs7485127	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers 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
9	nsv899491	chr12:104151560-104175575	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104155000-104178000	Weak transcription	Colonic Mucosa	Colon
4	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
5	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:104163000-104178400	Strong transcription	NHEK	skin
7	chr12:104163200-104175200	Weak transcription	Psoas Muscle	Psoas
8	chr12:104163600-104174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:104163600-104185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
12	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
13	chr12:104167000-104174400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:104167200-104176000	Weak transcription	Small Intestine	intestine
15	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:104168000-104176800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:104168000-104178800	Weak transcription	Hela-S3	cervix
18	chr12:104168000-104185200	Weak transcription	Brain Germinal Matrix	brain
19	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:104168600-104180800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr12:104168800-104174000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:104168800-104174000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr12:104168800-104174200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr12:104168800-104175400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:104169000-104174200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:104169000-104175000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:104169000-104176800	Strong transcription	Liver	Liver
28	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:104169200-104180200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:104169400-104174800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:104169600-104174200	Strong transcription	Colon Smooth Muscle	Colon
32	chr12:104169600-104184800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:104170200-104174400	Strong transcription	Fetal Stomach	stomach
34	chr12:104170400-104179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:104170400-104180400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr12:104170600-104174000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:104170600-104174000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:104170600-104174200	Strong transcription	Primary T cells from cord blood	blood
39	chr12:104170600-104174200	Strong transcription	Aorta	Aorta
40	chr12:104170600-104175000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr12:104170600-104175200	Strong transcription	Adipose Nuclei	Adipose
42	chr12:104170600-104177200	Strong transcription	Fetal Intestine Large	intestine
43	chr12:104170600-104179400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr12:104170800-104174400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:104170800-104174800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:104170800-104175800	Strong transcription	HepG2	liver
47	chr12:104170800-104176600	Strong transcription	Fetal Intestine Small	intestine
48	chr12:104171200-104174000	Strong transcription	Esophagus	oesophagus
49	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:104171400-104177800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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