Variant report

Variant	rs7869854
Chromosome Location	chr9:3363587-3363588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:3362011..3363818-chr9:3525245..3528041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232104	Chromatin interaction
ENSG00000080298	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10117357	0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10117431	0.88[JPT][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs10124292	0.86[JPT][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs10124295	0.86[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10511447	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10814019	0.85[AMR][1000 genomes]
rs10814038	0.96[YRI][hapmap]
rs10814039	0.90[YRI][hapmap]
rs10971534	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10971535	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10971599	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10971661	0.92[YRI][hapmap]
rs10971665	0.88[YRI][hapmap]
rs10971667	0.88[JPT][hapmap]
rs12002215	0.88[JPT][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs12335763	0.90[YRI][hapmap]
rs12338746	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13286511	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs13302664	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1348369	0.96[YRI][hapmap]
rs16917371	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986682	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35945655	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4237147	0.92[YRI][hapmap]
rs4741825	0.82[YRI][hapmap]
rs56829164	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66463406	0.83[ASN][1000 genomes]
rs7021584	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7022682	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026530	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029544	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043493	0.88[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7045360	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768485	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7858850	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860163	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870914	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875889	0.96[YRI][hapmap]
rs9298952	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv466091	chr9:3349487-3389660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv613146	chr9:3349487-3389660	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:3337800-3388800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr9:3341200-3397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
5	chr9:3354600-3364600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:3355000-3383800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:3355400-3365600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:3359400-3383200	Weak transcription	Primary T cells from cord blood	blood
9	chr9:3359400-3387600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:3359600-3369600	Weak transcription	Pancreas	Pancrea
11	chr9:3359600-3383800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:3359800-3364000	Weak transcription	Left Ventricle	heart
13	chr9:3359800-3365800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:3359800-3384000	Weak transcription	Primary B cells from cord blood	blood
15	chr9:3361200-3367000	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:3361200-3370600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr9:3361400-3367200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:3361800-3364000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr9:3362200-3363800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:3362200-3367000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:3362400-3363600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr9:3362400-3367200	Weak transcription	GM12878-XiMat	blood
23	chr9:3362800-3366800	Weak transcription	Brain Anterior Caudate	brain
24	chr9:3362800-3367200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:3363000-3367000	Weak transcription	Colon Smooth Muscle	Colon
26	chr9:3363200-3366800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:3363200-3367200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:3363200-3369000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:3363400-3367000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links