Variant report

Variant	rs3808895
Chromosome Location	chr9:100686554-100686555
allele	G/T
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	RAD21	chr9:100685640-100686601	HCT-116	colon:	n/a	chr9:100686169-100686183 chr9:100686170-100686177 chr9:100686168-100686187 chr9:100685917-100685936
2	CTCF	chr9:100685336-100686645	HCT-116	colon:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100685916-100685934 chr9:100686168-100686184 chr9:100685919-100685932 chr9:100686167-100686185
3	RAD21	chr9:100685590-100686567	MCF-7	breast:	n/a	chr9:100686169-100686183 chr9:100686170-100686177 chr9:100686168-100686187 chr9:100685917-100685936
4	CTCF	chr9:100686500-100686650	GM12872	blood:	n/a	n/a
5	POLR2A	chr9:100686213-100687319	PBDE	blood:	n/a	n/a
6	TBP	chr9:100685900-100686564	GM12878	blood:	n/a	n/a
7	CTCF	chr9:100684074-100686731	A549	lung:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100685916-100685934 chr9:100686168-100686184 chr9:100685919-100685932 chr9:100686167-100686185
8	TBL1XR1	chr9:100685310-100686884	K562	blood:	n/a	n/a
9	CTCF	chr9:100684091-100686626	SK-N-SH	brain:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100685916-100685934 chr9:100686168-100686184 chr9:100685919-100685932 chr9:100686167-100686185

No.	Distal block	Cell Line	Cell type
1	chr9:100682029..100688801-chr9:100740969..100749393,29	MCF-7	breast:
2	chr9:100685020..100686845-chr9:100716549..100717520,12	K562	blood:
3	chr9:100682922..100687440-chr9:100817123..100820939,8	MCF-7	breast:
4	chr9:100685586..100688165-chr9:100878796..100881297,2	K562	blood:
5	chr9:100685412..100687157-chr9:100698092..100700080,2	MCF-7	breast:
6	chr9:100685930..100687826-chr9:100769901..100771666,3	K562	blood:
7	chr9:100685576..100688537-chr9:100780625..100782385,2	K562	blood:
8	chr9:100684661..100686943-chr9:100794140..100799259,5	K562	blood:
9	chr9:100393929..100396893-chr9:100683273..100687162,3	K562	blood:
10	chr9:100684640..100686948-chr9:100880759..100882563,2	K562	blood:
11	chr9:100683337..100688322-chr9:101015638..101019207,5	MCF-7	breast:
12	chr9:100678422..100708679-chr9:100734559..100755577,174	K562	blood:
13	chr9:100685383..100686650-chr9:100796663..100797820,11	K562	blood:
14	chr9:100683079..100687048-chr9:101015405..101020638,4	K562	blood:
15	chr9:100685514..100687681-chr9:100731460..100733588,2	K562	blood:
16	chr9:100686261..100688755-chr9:100806613..100809213,2	K562	blood:
17	chr9:100682507..100691249-chr9:100739828..100748095,35	MCF-7	breast:
18	chr9:100685001..100687073-chr9:100804782..100806329,2	K562	blood:
19	chr9:100684278..100686693-chr9:100816052..100820620,8	K562	blood:
20	chr2:131894199..131896837-chr9:100685147..100687682,2	MCF-7	breast:
21	chr9:100685127..100688021-chr9:100778345..100779899,2	MCF-7	breast:
22	chr9:100686277..100688519-chr9:100689376..100691185,2	MCF-7	breast:
23	chr9:100675954..100709047-chr9:100737887..100755543,175	K562	blood:
24	chr9:100686308..100689678-chr9:101021142..101024168,3	MCF-7	breast:
25	chr9:100685496..100686599-chr9:101025791..101026677,7	MCF-7	breast:
26	chr9:100683227..100687367-chr9:100758311..100762778,5	K562	blood:

Variant related genes	Relation type
C9orf156	TF binding region
ENSG00000095380	Chromatin interaction
ENSG00000095383	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000136925	Chromatin interaction
ENSG00000236896	Chromatin interaction
ENSG00000212521	Chromatin interaction
ENSG00000106785	Chromatin interaction
ENSG00000136937	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1007506	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10115216	0.90[CHB][hapmap]
rs10512255	0.90[CHB][hapmap]
rs10739526	0.90[CHB][hapmap]
rs10818284	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10984079	0.86[ASN][1000 genomes]
rs10984134	0.86[ASN][1000 genomes]
rs10984156	0.86[ASN][1000 genomes]
rs10984195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10984218	0.90[ASN][1000 genomes]
rs10984222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10984253	0.90[CHB][hapmap]
rs10984311	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10984393	0.95[ASN][1000 genomes]
rs10984421	0.84[ASN][1000 genomes]
rs10984422	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10984424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10984481	1.00[JPT][hapmap]
rs10984510	1.00[JPT][hapmap]
rs12004762	0.90[CHB][hapmap]
rs12006522	0.90[CHB][hapmap]
rs12342417	0.90[CHB][hapmap]
rs1561957	0.90[CHB][hapmap]
rs1561961	0.90[CHB][hapmap]
rs2120262	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2282190	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs28417086	0.90[ASN][1000 genomes]
rs28697997	0.90[ASN][1000 genomes]
rs3021525	0.88[ASN][1000 genomes]
rs3758250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3808893	0.90[CHB][hapmap]
rs3824495	0.90[CHB][hapmap]
rs4743149	1.00[JPT][hapmap]
rs7031386	0.90[CHB][hapmap]
rs7034336	0.86[CHB][hapmap]
rs7036589	0.90[CHB][hapmap]
rs7037324	0.90[CHB][hapmap]
rs7038998	0.89[CHB][hapmap]
rs7048255	1.00[CHB][hapmap]
rs72753537	0.86[ASN][1000 genomes]
rs9299258	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3808895	Hs.43687	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100684000-100686600	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr9:100684000-100687200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr9:100685000-100687000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr9:100685000-100687200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:100685000-100687200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr9:100685200-100687600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:100685400-100686600	Flanking Active TSS	Dnd41	blood
8	chr9:100685400-100687800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr9:100685600-100686600	Enhancers	Colon Smooth Muscle	Colon
10	chr9:100685600-100687200	Enhancers	Primary B cells from peripheral blood	blood
11	chr9:100685800-100686600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:100686000-100686600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr9:100686000-100686800	Enhancers	Hela-S3	cervix
14	chr9:100686000-100687000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr9:100686000-100687400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr9:100686200-100686600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr9:100686200-100686600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr9:100686200-100686600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:100686200-100686600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:100686200-100686600	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr9:100686200-100686600	Flanking Active TSS	K562	blood
22	chr9:100686200-100686800	Weak transcription	Brain Substantia Nigra	brain
23	chr9:100686200-100686800	Weak transcription	Fetal Thymus	thymus
24	chr9:100686200-100687200	Enhancers	Primary T cells from cord blood	blood
25	chr9:100686200-100690800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr9:100686200-100691400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:100686200-100692200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr9:100686200-100692200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:100686400-100686600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:100686400-100686600	Active TSS	Primary B cells from cord blood	blood
31	chr9:100686400-100686600	Enhancers	Brain Anterior Caudate	brain
32	chr9:100686400-100686600	Enhancers	Brain Cingulate Gyrus	brain
33	chr9:100686400-100686600	Enhancers	Brain Hippocampus Middle	brain
34	chr9:100686400-100686600	Weak transcription	Thymus	Thymus
35	chr9:100686400-100686600	Flanking Bivalent TSS/Enh	A549	lung
36	chr9:100686400-100686800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr9:100686400-100686800	Enhancers	Brain Angular Gyrus	brain
38	chr9:100686400-100686800	Enhancers	HepG2	liver
39	chr9:100686400-100687200	Enhancers	GM12878-XiMat	blood
40	chr9:100686400-100690800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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