Variant report

Variant	rs6987277
Chromosome Location	chr8:8939831-8939832
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:8931416..8936474-chr8:8938271..8941320,7	K562	blood:
2	chr8:8932762..8934557-chr8:8938134..8939929,2	MCF-7	breast:
3	chr8:8939297..8940892-chr8:9008509..9010684,2	K562	blood:
4	chr8:8935137..8938110-chr8:8938203..8940506,3	MCF-7	breast:
5	chr8:8938481..8944528-chr8:8944977..8948023,6	K562	blood:

Variant related genes	Relation type
ENSG00000253426	Chromatin interaction
ENSG00000173281	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11774329	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17155176	0.84[ASW][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap]
rs17155179	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17155181	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6601286	1.00[CEU][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7818455	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7825188	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv518456	chr8:8939125-8948469	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6987277	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8929600-8940000	Weak transcription	Aorta	Aorta
2	chr8:8930200-8940400	Enhancers	Fetal Intestine Large	intestine
3	chr8:8931800-8940800	Enhancers	Fetal Intestine Small	intestine
4	chr8:8932600-8951800	Weak transcription	Pancreas	Pancrea
5	chr8:8932800-8945600	Weak transcription	Thymus	Thymus
6	chr8:8934200-8940000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr8:8935400-8959600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr8:8935800-8940000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr8:8936000-8940400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr8:8936200-8940000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr8:8936200-8940400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr8:8936400-8940400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr8:8937400-8940400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr8:8937400-8940600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr8:8937400-8943400	Enhancers	Hela-S3	cervix
16	chr8:8937800-8940400	Enhancers	Small Intestine	intestine
17	chr8:8937800-8940800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr8:8937800-8940800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr8:8938000-8940400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr8:8938000-8940400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr8:8938000-8945200	Weak transcription	Placenta	Placenta
22	chr8:8938000-8951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:8938200-8940400	Enhancers	Duodenum Mucosa	Duodenum
24	chr8:8938200-8940400	Enhancers	Stomach Mucosa	stomach
25	chr8:8938400-8940000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr8:8938400-8940000	Weak transcription	Colonic Mucosa	Colon
27	chr8:8938400-8940400	Enhancers	Fetal Heart	heart
28	chr8:8938400-8945200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr8:8938400-8945200	Weak transcription	Primary B cells from cord blood	blood
30	chr8:8938400-8945200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr8:8938600-8940400	Enhancers	NHEK	skin
32	chr8:8938800-8940000	Weak transcription	Left Ventricle	heart
33	chr8:8938800-8940400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr8:8938800-8940400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr8:8938800-8940400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr8:8939000-8940400	Enhancers	HMEC	breast
37	chr8:8939000-8940400	Enhancers	Osteobl	bone
38	chr8:8939200-8940000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr8:8939200-8940400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr8:8939200-8940400	Enhancers	Adipose Nuclei	Adipose
41	chr8:8939200-8940600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:8939400-8940000	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr8:8939400-8940000	Enhancers	Brain Anterior Caudate	brain
44	chr8:8939400-8940000	Enhancers	Fetal Lung	lung
45	chr8:8939400-8940000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr8:8939400-8940200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr8:8939400-8940200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:8939400-8940200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr8:8939400-8940200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr8:8939400-8940200	Flanking Active TSS	A549	lung

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