Variant report

Variant	rs10121671
Chromosome Location	chr9:2838107-2838108
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2828822..2830998-chr9:2836567..2839004,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000080608	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10116824	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10125846	0.83[CEU][hapmap]
rs10217194	0.87[CEU][hapmap]
rs10481516	0.82[CEU][hapmap];0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs10733432	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10738791	0.87[CEU][hapmap]
rs10757715	0.87[CEU][hapmap]
rs10812770	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10968361	0.87[CEU][hapmap]
rs11790146	0.85[CHB][hapmap]
rs3824351	0.81[CHB][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4439183	0.82[CEU][hapmap]
rs4741768	0.86[CHB][hapmap]
rs4741769	0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6476038	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6476047	0.96[CEU][hapmap];0.87[EUR][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	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892079	chr9:2681430-2931341	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv892081	chr9:2691186-2851026	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1028011	chr9:2759097-2904277	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1022873	chr9:2768825-2863264	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv892083	chr9:2809548-2900651	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr9:2801200-2838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:2811600-2842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:2814800-2838200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:2815600-2838200	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr9:2819600-2838200	Weak transcription	Fetal Heart	heart
6	chr9:2819600-2841800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:2822200-2838800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:2822400-2838400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:2822400-2838600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:2824000-2838200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:2824000-2838600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:2824000-2838800	Strong transcription	Dnd41	blood
13	chr9:2825000-2838200	Strong transcription	A549	lung
14	chr9:2825600-2839200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:2828600-2843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:2830000-2838400	Weak transcription	Stomach Mucosa	stomach
17	chr9:2830000-2842400	Weak transcription	Thymus	Thymus
18	chr9:2830200-2839600	Weak transcription	Small Intestine	intestine
19	chr9:2830800-2842800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr9:2834200-2838800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:2834400-2842400	Weak transcription	Fetal Brain Male	brain
22	chr9:2834400-2843000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr9:2834800-2838400	Weak transcription	Brain Substantia Nigra	brain
24	chr9:2836400-2838200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:2836400-2838400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:2836400-2842600	Weak transcription	Fetal Intestine Small	intestine
27	chr9:2836600-2842800	Weak transcription	Aorta	Aorta
28	chr9:2836800-2838200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:2836800-2838200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:2836800-2838600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr9:2836800-2839200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:2836800-2842000	Weak transcription	Right Ventricle	heart
33	chr9:2836800-2842200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:2836800-2843200	Weak transcription	Gastric	stomach
35	chr9:2836800-2843400	Weak transcription	Spleen	Spleen
36	chr9:2837200-2838200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:2837200-2838200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr9:2837200-2838200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:2837200-2838200	Weak transcription	Brain Anterior Caudate	brain
40	chr9:2837200-2838200	Weak transcription	Ovary	ovary
41	chr9:2837200-2838200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr9:2837200-2838200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr9:2837200-2838200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr9:2837200-2838200	Weak transcription	HSMMtube	muscle
45	chr9:2837200-2838400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr9:2837200-2838400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr9:2837200-2838400	Weak transcription	HSMM	muscle
48	chr9:2837200-2838600	Weak transcription	HMEC	breast
49	chr9:2837200-2838800	Weak transcription	Brain Germinal Matrix	brain
50	chr9:2837200-2839200	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links