Variant report

Variant	rs4077177
Chromosome Location	chr9:95827409-95827410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr9:95826470-95827454	GM12878	blood:	n/a	n/a
2	ESRRA	chr9:95825379-95827466	GM12878	blood:	n/a	chr9:95826281-95826295 chr9:95826280-95826296 chr9:95826863-95826879 chr9:95826863-95826879 chr9:95826279-95826297 chr9:95825948-95825958 chr9:95826735-95826751 chr9:95826281-95826300
3	PML	chr9:95826453-95827494	GM12878	blood:	n/a	chr9:95827238-95827246
4	POLR2A	chr9:95826619-95827459	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:95826540-95827497	GM18505	blood:	n/a	n/a
6	CHD2	chr9:95826565-95827491	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95826956..95829616-chr9:95830971..95832502,2	K562	blood:
2	chr9:95824581..95826118-chr9:95826533..95829514,2	MCF-7	breast:
3	chr9:95825270..95827646-chr9:95832621..95835628,3	K562	blood:

Variant related genes	Relation type
SUSD3	TF binding region
ENSG00000157303	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10821063	0.84[ASN][1000 genomes]
rs10992622	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992623	0.81[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1131773	0.85[CHD][hapmap]
rs12375973	0.81[CEU][hapmap];0.82[CHD][hapmap]
rs12555029	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077176	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077637	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077811	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs4078501	0.86[GIH][hapmap];0.92[JPT][hapmap]
rs4341217	0.92[CHD][hapmap];0.91[JPT][hapmap]
rs4636265	0.85[CHD][hapmap]
rs56000948	0.92[ASN][1000 genomes]
rs56868344	0.93[AFR][1000 genomes]
rs57327517	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57408424	0.93[AFR][1000 genomes]
rs57974003	0.91[AFR][1000 genomes]
rs60671060	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479448	0.80[ASN][1000 genomes]
rs7019574	0.89[ASN][1000 genomes]
rs7025686	0.85[CHD][hapmap]
rs7036869	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046192	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7046328	0.85[CHB][hapmap]
rs7859109	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7870697	0.92[ASN][1000 genomes]
rs7870953	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9696357	0.89[CEU][hapmap];0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893575	chr9:95781040-95854013	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4077177	SUSD3	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95820800-95827600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr9:95821600-95827600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
3	chr9:95822000-95834200	Weak transcription	Esophagus	oesophagus
4	chr9:95822000-95834200	Weak transcription	Right Atrium	heart
5	chr9:95822400-95828600	Enhancers	Primary hematopoietic stem cells	blood
6	chr9:95822600-95834400	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:95822800-95831000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:95823400-95827800	Weak transcription	Right Ventricle	heart
9	chr9:95824000-95833800	Weak transcription	Ovary	ovary
10	chr9:95824600-95854000	Weak transcription	Gastric	stomach
11	chr9:95824800-95833200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:95825200-95829000	Weak transcription	Pancreas	Pancrea
13	chr9:95825200-95834000	Weak transcription	Liver	Liver
14	chr9:95825400-95827600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr9:95825400-95828200	Enhancers	Duodenum Mucosa	Duodenum
16	chr9:95825600-95827800	Enhancers	Spleen	Spleen
17	chr9:95825800-95828600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr9:95826000-95827800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr9:95826200-95828000	Weak transcription	Brain Substantia Nigra	brain
20	chr9:95826200-95828400	Strong transcription	Fetal Intestine Small	intestine
21	chr9:95826400-95828400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr9:95826600-95828000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr9:95826600-95828200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:95826600-95828200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr9:95826600-95828400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:95826800-95828000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:95826800-95828200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:95826800-95828200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr9:95826800-95828400	Enhancers	Adipose Nuclei	Adipose
30	chr9:95827000-95827600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr9:95827000-95827600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:95827000-95827800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr9:95827000-95827800	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr9:95827000-95827800	Weak transcription	Left Ventricle	heart
35	chr9:95827000-95828000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:95827000-95828200	Enhancers	Fetal Muscle Leg	muscle
37	chr9:95827000-95828400	Enhancers	Placenta	Placenta
38	chr9:95827000-95828400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr9:95827200-95827800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:95827200-95827800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr9:95827200-95827800	Enhancers	Lung	lung
42	chr9:95827200-95828000	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr9:95827200-95828000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr9:95827200-95828800	Genic enhancers	Primary B cells from cord blood	blood
45	chr9:95827400-95827600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
46	chr9:95827400-95827600	Genic enhancers	GM12878-XiMat	blood
47	chr9:95827400-95828000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:95827400-95828000	Enhancers	Colonic Mucosa	Colon
49	chr9:95827400-95828200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:95827400-95828400	Genic enhancers	Primary B cells from peripheral blood	blood

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