Variant report

Variant	rs4647559
Chromosome Location	chr9:97861904-97861905
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97487666..97489683-chr9:97860504..97862653,2	MCF-7	breast:
2	chr7:155653017..155655598-chr9:97861454..97863217,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs242448	0.84[YRI][hapmap]
rs356659	0.92[YRI][hapmap]
rs356661	0.84[YRI][hapmap]
rs356686	0.84[YRI][hapmap]
rs4744443	0.84[YRI][hapmap]
rs57232080	0.81[AFR][1000 genomes]
rs58038897	0.81[AFR][1000 genomes]
rs60070508	0.81[AFR][1000 genomes]
rs640628	0.92[YRI][hapmap]
rs646350	0.86[YRI][hapmap]
rs7032542	0.81[AFR][1000 genomes]
rs7032704	0.81[AFR][1000 genomes]
rs73654506	0.81[AFR][1000 genomes]
rs73654507	0.81[AFR][1000 genomes]
rs73654508	0.81[AFR][1000 genomes]
rs73654509	0.81[AFR][1000 genomes]
rs73654510	0.81[AFR][1000 genomes]
rs73654511	0.81[AFR][1000 genomes]
rs73654513	0.81[AFR][1000 genomes]
rs73654514	0.81[AFR][1000 genomes]
rs73654516	0.81[AFR][1000 genomes]
rs73654517	0.95[AFR][1000 genomes]
rs73654518	1.00[AFR][1000 genomes]
rs73654519	0.92[AFR][1000 genomes]
rs73654520	1.00[AFR][1000 genomes]
rs73654521	1.00[AFR][1000 genomes]
rs73654522	1.00[AFR][1000 genomes]
rs73654523	1.00[AFR][1000 genomes]
rs73654525	1.00[AFR][1000 genomes]
rs73654526	1.00[AFR][1000 genomes]
rs73654528	1.00[AFR][1000 genomes]
rs7866396	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4647559	FAM48B2	trans	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
7	chr9:97847600-97878400	Weak transcription	Dnd41	blood
8	chr9:97849200-97863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:97849800-97864600	Enhancers	Psoas Muscle	Psoas
10	chr9:97850000-97862000	Weak transcription	Hela-S3	cervix
11	chr9:97854200-97862200	Weak transcription	Aorta	Aorta
12	chr9:97854200-97862200	Weak transcription	HepG2	liver
13	chr9:97854200-97862400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:97855000-97867800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr9:97855200-97876800	Weak transcription	GM12878-XiMat	blood
16	chr9:97855400-97862200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:97855400-97865400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:97855400-97884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:97855600-97862200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr9:97855600-97862400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:97855600-97862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:97855600-97863200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:97855600-97865400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr9:97855600-97876400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr9:97855600-97878600	Weak transcription	Stomach Mucosa	stomach
26	chr9:97856200-97862000	Weak transcription	NHDF-Ad	bronchial
27	chr9:97856200-97862200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr9:97856200-97862200	Weak transcription	Osteobl	bone
29	chr9:97856200-97872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:97856400-97862600	Genic enhancers	Right Ventricle	heart
31	chr9:97856600-97862200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:97856600-97862400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:97856600-97865200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:97857000-97862200	Weak transcription	Primary T cells from cord blood	blood
35	chr9:97857400-97862200	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:97857400-97862800	Genic enhancers	A549	lung
37	chr9:97857800-97869600	Weak transcription	HUVEC	blood vessel
38	chr9:97858000-97862000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:97858000-97862200	Weak transcription	Brain Substantia Nigra	brain
40	chr9:97858000-97862800	Weak transcription	Brain Anterior Caudate	brain
41	chr9:97858000-97863400	Strong transcription	Colonic Mucosa	Colon
42	chr9:97858000-97863800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:97858200-97862000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:97858400-97862400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr9:97858600-97863000	Weak transcription	Brain Hippocampus Middle	brain
46	chr9:97858600-97867600	Genic enhancers	Fetal Muscle Leg	muscle
47	chr9:97858600-97877200	Strong transcription	Fetal Intestine Large	intestine
48	chr9:97858600-97878400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr9:97858800-97862000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr9:97858800-97863800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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