Variant report

Variant	rs28657441
Chromosome Location	chr9:137004991-137004992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136932690..136935080-chr9:137003441..137005032,2	MCF-7	breast:
2	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
3	chr9:137003283..137007180-chr9:137027026..137030232,3	K562	blood:

Variant related genes	Relation type
ENSG00000221676	Chromatin interaction
ENSG00000169925	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28377785	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28421319	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28425680	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434714	1.00[EUR][1000 genomes]
rs28436125	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28488634	1.00[EUR][1000 genomes]
rs28538491	1.00[EUR][1000 genomes]
rs28540578	1.00[EUR][1000 genomes]
rs28562287	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28565058	1.00[EUR][1000 genomes]
rs28585632	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28593202	1.00[EUR][1000 genomes]
rs28594106	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595141	1.00[EUR][1000 genomes]
rs28626085	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28626885	1.00[EUR][1000 genomes]
rs28637300	1.00[EUR][1000 genomes]
rs28654988	1.00[EUR][1000 genomes]
rs28673958	1.00[EUR][1000 genomes]
rs28687115	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28687158	0.96[EUR][1000 genomes]
rs28701738	1.00[EUR][1000 genomes]
rs28705949	1.00[EUR][1000 genomes]
rs28715994	1.00[EUR][1000 genomes]
rs28733640	1.00[EUR][1000 genomes]
rs28756160	1.00[EUR][1000 genomes]
rs28759300	1.00[EUR][1000 genomes]
rs34022301	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34031108	1.00[EUR][1000 genomes]
rs34062061	1.00[EUR][1000 genomes]
rs34169579	1.00[EUR][1000 genomes]
rs34259931	0.89[EUR][1000 genomes]
rs34350861	1.00[EUR][1000 genomes]
rs34515929	1.00[EUR][1000 genomes]
rs34523253	1.00[EUR][1000 genomes]
rs34856382	1.00[EUR][1000 genomes]
rs35158191	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35237188	1.00[EUR][1000 genomes]
rs35370793	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35420166	1.00[EUR][1000 genomes]
rs35874066	0.87[AMR][1000 genomes]
rs35962164	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35985804	0.92[EUR][1000 genomes]
rs36029182	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking 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	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137002400-137005600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:137002400-137006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:137002400-137016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:137002600-137005000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:137002600-137005000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:137002600-137005000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:137002600-137005000	Enhancers	Pancreas	Pancrea
8	chr9:137002600-137005200	Genic enhancers	Fetal Intestine Small	intestine
9	chr9:137002600-137005800	Genic enhancers	Fetal Stomach	stomach
10	chr9:137003000-137005200	Weak transcription	K562	blood
11	chr9:137003200-137005600	Genic enhancers	Fetal Muscle Trunk	muscle
12	chr9:137003200-137005800	Genic enhancers	Fetal Muscle Leg	muscle
13	chr9:137003200-137024200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:137003600-137005200	Weak transcription	Primary B cells from cord blood	blood
15	chr9:137003600-137007600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:137003600-137024800	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr9:137003800-137005000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:137003800-137005000	Weak transcription	Placenta	Placenta
19	chr9:137003800-137005000	Weak transcription	Thymus	Thymus
20	chr9:137003800-137005200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr9:137003800-137007000	Weak transcription	Stomach Mucosa	stomach
22	chr9:137004000-137005000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:137004000-137005800	Weak transcription	NH-A	brain
24	chr9:137004000-137017400	Strong transcription	HUVEC	blood vessel
25	chr9:137004000-137024000	Strong transcription	A549	lung
26	chr9:137004000-137024800	Strong transcription	Primary T cells from cord blood	blood
27	chr9:137004200-137005000	Enhancers	Fetal Lung	lung
28	chr9:137004200-137005200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:137004200-137005200	Genic enhancers	Lung	lung
30	chr9:137004200-137005600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:137004200-137005600	Weak transcription	Colonic Mucosa	Colon
32	chr9:137004200-137006600	Weak transcription	Fetal Kidney	kidney
33	chr9:137004200-137007400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr9:137004200-137015800	Weak transcription	Fetal Heart	heart
35	chr9:137004200-137016000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:137004200-137024400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:137004200-137024800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr9:137004200-137024800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr9:137004200-137025000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr9:137004200-137025000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr9:137004200-137026000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:137004400-137005000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:137004400-137005000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:137004400-137005000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:137004400-137005000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr9:137004400-137005000	Weak transcription	Aorta	Aorta
47	chr9:137004400-137005000	Enhancers	HepG2	liver
48	chr9:137004400-137005200	Weak transcription	Right Ventricle	heart
49	chr9:137004400-137005200	Weak transcription	GM12878-XiMat	blood
50	chr9:137004400-137005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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