Variant report

Variant	rs10938546
Chromosome Location	chr4:48907396-48907397
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48907349..48910637-chr4:48932106..48935377,4	MCF-7	breast:
2	chr4:48907213..48908063-chr4:48944694..48945681,2	MCF-7	breast:
3	chr4:48899707..48901382-chr4:48907101..48909045,2	K562	blood:
4	chr4:48779823..48782624-chr4:48905090..48909886,4	MCF-7	breast:
5	chr4:48700525..48703151-chr4:48906796..48908721,2	MCF-7	breast:
6	chr4:48832331..48834187-chr4:48907329..48910001,2	MCF-7	breast:
7	chr4:48831616..48834377-chr4:48906971..48910422,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145247	Chromatin interaction
ENSG00000109180	Chromatin interaction
ENSG00000252913	Chromatin interaction
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1517675	1.00[CHB][hapmap]
rs17610725	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17656727	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17656763	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1824039	0.85[YRI][hapmap]
rs2304387	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2354947	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605248	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45463191	1.00[ASN][1000 genomes]
rs62310925	1.00[ASN][1000 genomes]
rs6447674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73815372	1.00[ASN][1000 genomes]
rs746513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48879400-48907800	Weak transcription	Right Ventricle	heart
2	chr4:48891200-48907800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:48891200-48907800	Weak transcription	Fetal Lung	lung
4	chr4:48891400-48907800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:48892200-48907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:48893200-48908000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:48893800-48907800	Weak transcription	Adipose Nuclei	Adipose
8	chr4:48894000-48907800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:48895000-48908000	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:48897800-48908000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:48899400-48907600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:48899600-48907800	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:48899800-48908000	Weak transcription	Small Intestine	intestine
14	chr4:48901200-48907400	Strong transcription	Primary B cells from cord blood	blood
15	chr4:48901800-48907400	Weak transcription	Fetal Heart	heart
16	chr4:48902400-48907800	Weak transcription	Brain Angular Gyrus	brain
17	chr4:48902400-48907800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:48902400-48907800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:48902400-48908000	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:48902400-48908000	Weak transcription	Brain Substantia Nigra	brain
21	chr4:48902400-48908200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:48902400-48908200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:48902600-48907800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:48903800-48907600	Enhancers	Placenta	Placenta
25	chr4:48904600-48907600	Weak transcription	NHLF	lung
26	chr4:48904600-48907800	Weak transcription	HSMM	muscle
27	chr4:48904800-48907600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:48904800-48907600	Weak transcription	Esophagus	oesophagus
29	chr4:48904800-48907600	Weak transcription	Lung	lung
30	chr4:48904800-48907600	Weak transcription	Spleen	Spleen
31	chr4:48904800-48908000	Weak transcription	Left Ventricle	heart
32	chr4:48904800-48908000	Weak transcription	Ovary	ovary
33	chr4:48904800-48908200	Weak transcription	Aorta	Aorta
34	chr4:48905000-48907800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:48905200-48907600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:48905200-48907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:48905400-48907400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:48905400-48907400	Weak transcription	Fetal Brain Female	brain
39	chr4:48905400-48907600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:48905400-48907600	Weak transcription	Fetal Kidney	kidney
41	chr4:48905400-48907800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr4:48906200-48907400	Genic enhancers	Dnd41	blood
43	chr4:48906200-48907600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:48906200-48907800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:48906200-48907800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:48906200-48907800	Enhancers	Fetal Brain Male	brain
47	chr4:48906400-48907600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr4:48906400-48907800	Weak transcription	Fetal Stomach	stomach
49	chr4:48906600-48907400	Genic enhancers	Fetal Intestine Small	intestine
50	chr4:48906600-48907400	Enhancers	Thymus	Thymus

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