Variant report

Variant	rs4647558
Chromosome Location	chr9:97862118-97862119
allele	A/G
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: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10115247	0.91[EUR][1000 genomes]
rs1011784	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10739992	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739993	0.82[EUR][1000 genomes]
rs10761374	0.86[JPT][hapmap]
rs10761377	0.84[EUR][1000 genomes]
rs10821447	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10821451	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821453	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821454	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821455	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10993490	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13295862	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17686583	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1979022	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2166402	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2282216	0.92[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2297596	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2297597	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2404457	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3277	0.85[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34045846	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34532504	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3737142	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3780561	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3780562	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3780564	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3780567	0.92[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs3780568	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3824486	0.92[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs3844341	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3852402	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4647382	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap]
rs4647443	0.86[EUR][1000 genomes]
rs4647459	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4647462	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647475	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4647528	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647529	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4647534	0.92[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs4647554	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4657	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4743988	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4744442	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4744446	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4744451	0.92[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs6479601	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7023007	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7034538	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7042293	0.81[JPT][hapmap]
rs7042320	0.82[JPT][hapmap]
rs7046682	0.91[JPT][hapmap]
rs7850958	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7854570	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7872648	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7874310	0.89[EUR][1000 genomes]
rs7874388	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs879492	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs881791	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs963774	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

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
rs4647558	SYK	cis	parietal	SCAN

Chromatin state (count:111 , 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	chr9:97854200-97862200	Weak transcription	Aorta	Aorta
11	chr9:97854200-97862200	Weak transcription	HepG2	liver
12	chr9:97854200-97862400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:97855000-97867800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr9:97855200-97876800	Weak transcription	GM12878-XiMat	blood
15	chr9:97855400-97862200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:97855400-97865400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:97855400-97884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:97855600-97862200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr9:97855600-97862400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:97855600-97862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:97855600-97863200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:97855600-97865400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:97855600-97876400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:97855600-97878600	Weak transcription	Stomach Mucosa	stomach
25	chr9:97856200-97862200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:97856200-97862200	Weak transcription	Osteobl	bone
27	chr9:97856200-97872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:97856400-97862600	Genic enhancers	Right Ventricle	heart
29	chr9:97856600-97862200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:97856600-97862400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:97856600-97865200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:97857000-97862200	Weak transcription	Primary T cells from cord blood	blood
33	chr9:97857400-97862200	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:97857400-97862800	Genic enhancers	A549	lung
35	chr9:97857800-97869600	Weak transcription	HUVEC	blood vessel
36	chr9:97858000-97862200	Weak transcription	Brain Substantia Nigra	brain
37	chr9:97858000-97862800	Weak transcription	Brain Anterior Caudate	brain
38	chr9:97858000-97863400	Strong transcription	Colonic Mucosa	Colon
39	chr9:97858000-97863800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:97858400-97862400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:97858600-97863000	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:97858600-97867600	Genic enhancers	Fetal Muscle Leg	muscle
43	chr9:97858600-97877200	Strong transcription	Fetal Intestine Large	intestine
44	chr9:97858600-97878400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr9:97858800-97863800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:97858800-97870800	Genic enhancers	Fetal Muscle Trunk	muscle
47	chr9:97859000-97863200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:97859000-97865400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
49	chr9:97859200-97862400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr9:97859200-97862600	Strong transcription	Fetal Brain Female	brain

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