Variant report

Variant	rs9840331
Chromosome Location	chr3:51405018-51405019
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	chr3:51404406..51407257-chr3:51420793..51424022,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12330534	1.00[AMR][1000 genomes]
rs12493978	0.88[YRI][hapmap]
rs13314120	1.00[AMR][1000 genomes]
rs13321674	1.00[AMR][1000 genomes]
rs13433729	0.85[AMR][1000 genomes]
rs17051799	1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051832	1.00[AMR][1000 genomes]
rs1842394	0.83[YRI][hapmap]
rs28421789	0.85[AMR][1000 genomes]
rs28452990	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28457212	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28653367	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2883900	0.85[AMR][1000 genomes]
rs4468966	0.89[YRI][hapmap]
rs4549265	1.00[AMR][1000 genomes]
rs58807639	1.00[ASN][1000 genomes]
rs59525691	1.00[AMR][1000 genomes]
rs60823123	1.00[AMR][1000 genomes]
rs72951441	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951452	1.00[AMR][1000 genomes]
rs72951472	1.00[AMR][1000 genomes]
rs72951485	1.00[AMR][1000 genomes]
rs72951486	1.00[AMR][1000 genomes]
rs72953413	0.85[AMR][1000 genomes]
rs751076	0.89[YRI][hapmap]
rs753452	1.00[ASN][1000 genomes]
rs880478	0.84[YRI][hapmap]
rs904144	0.85[AMR][1000 genomes]
rs9311470	0.85[AMR][1000 genomes]
rs9808940	0.85[AMR][1000 genomes]
rs9809757	1.00[AMR][1000 genomes]
rs9812008	1.00[AMR][1000 genomes]
rs9815684	1.00[AMR][1000 genomes]
rs9816075	1.00[AMR][1000 genomes]
rs9817077	0.89[YRI][hapmap]
rs9817872	0.89[YRI][hapmap]
rs9819195	0.89[YRI][hapmap]
rs9824779	1.00[AMR][1000 genomes]
rs9826664	0.85[AMR][1000 genomes]
rs9827665	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827917	1.00[AMR][1000 genomes]
rs9829057	0.89[YRI][hapmap]
rs9838294	1.00[AMR][1000 genomes]
rs9838942	1.00[AMR][1000 genomes]
rs9838994	1.00[AMR][1000 genomes]
rs9839516	0.85[AMR][1000 genomes]
rs9839608	1.00[AMR][1000 genomes]
rs9844541	1.00[AMR][1000 genomes]
rs9855809	0.85[AMR][1000 genomes]
rs9856134	0.83[YRI][hapmap]
rs9857893	1.00[AMR][1000 genomes]
rs9858497	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9864213	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866513	1.00[AMR][1000 genomes]
rs9866604	0.85[AMR][1000 genomes]
rs9870147	1.00[AMR][1000 genomes]
rs9880909	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9881402	1.00[AMR][1000 genomes]
rs9881844	1.00[AMR][1000 genomes]
rs9882601	1.00[AMR][1000 genomes]
rs9990341	1.00[AMR][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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv460534	chr3:51393046-51416108	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv590274	chr3:51393046-51416108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv460535	chr3:51395571-51416108	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv590275	chr3:51395571-51416108	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
3	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
4	chr3:51384200-51420600	Weak transcription	Fetal Brain Male	brain
5	chr3:51385400-51405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:51386400-51405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:51391600-51406800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:51392800-51418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:51393200-51405600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:51394000-51405400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:51394600-51405400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:51398800-51405800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:51399400-51405600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:51400200-51405600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:51400200-51405600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:51400400-51405600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:51400400-51405600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:51400400-51405600	Weak transcription	Brain Germinal Matrix	brain
19	chr3:51400400-51405600	Weak transcription	Fetal Brain Female	brain
20	chr3:51400600-51411400	Weak transcription	Brain Anterior Caudate	brain
21	chr3:51400800-51405400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:51400800-51405400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:51400800-51405400	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:51400800-51405600	Weak transcription	Brain Angular Gyrus	brain
25	chr3:51400800-51408200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:51400800-51410800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:51400800-51411000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:51400800-51411400	Weak transcription	Brain Substantia Nigra	brain
29	chr3:51400800-51411400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:51400800-51412200	Weak transcription	HSMMtube	muscle
31	chr3:51401000-51411800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:51404800-51406400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links