Variant report

Variant	rs1619327
Chromosome Location	chr6:37599093-37599094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37575521..37577544-chr6:37596904..37599235,2	K562	blood:
2	chr6:37597500..37600004-chr6:37601330..37604250,3	K562	blood:
3	chr6:37598980..37601085-chr6:37607743..37610334,2	K562	blood:
4	chr6:37592829..37595564-chr6:37597179..37600558,4	MCF-7	breast:
5	chr6:37596331..37599746-chr6:37605626..37607934,3	MCF-7	breast:
6	chr6:37590156..37593424-chr6:37597234..37601597,4	K562	blood:

Variant related genes	Relation type
ENSG00000112139	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10485031	1.00[CHB][hapmap]
rs10755699	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs1738454	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17639655	1.00[CHB][hapmap]
rs1776447	1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs3846877	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs3887743	1.00[CHB][hapmap]
rs4236057	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs6911875	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs6915583	1.00[CHB][hapmap]
rs6922589	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs804828	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804840	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs804841	1.00[CHB][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs9380696	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv602955	chr6:37581200-37599962	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1619327	FGD2	cis	parietal	SCAN
rs1619327	KIF6	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37594000-37615400	Weak transcription	Fetal Brain Female	brain
2	chr6:37594200-37602200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:37595600-37599200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:37595600-37599200	Enhancers	NHEK	skin
5	chr6:37595600-37599200	Enhancers	NHLF	lung
6	chr6:37595600-37599400	Enhancers	NHDF-Ad	bronchial
7	chr6:37595800-37599200	Enhancers	Osteobl	bone
8	chr6:37595800-37599400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:37595800-37599400	Enhancers	HSMM	muscle
10	chr6:37595800-37599400	Enhancers	NH-A	brain
11	chr6:37596000-37599200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:37596000-37599400	Enhancers	HUVEC	blood vessel
13	chr6:37596600-37599400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:37596600-37599400	Enhancers	HMEC	breast
15	chr6:37597000-37599400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:37597200-37599800	Enhancers	Hela-S3	cervix
17	chr6:37597400-37599600	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr6:37597600-37599400	Enhancers	K562	blood
19	chr6:37597800-37599200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:37597800-37599200	Enhancers	Esophagus	oesophagus
21	chr6:37597800-37599400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:37597800-37599800	Enhancers	Spleen	Spleen
23	chr6:37598400-37599200	Weak transcription	Right Atrium	heart
24	chr6:37598400-37599800	Enhancers	Primary B cells from peripheral blood	blood
25	chr6:37598600-37599200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:37598600-37599600	Enhancers	GM12878-XiMat	blood
27	chr6:37598600-37599800	Enhancers	Primary B cells from cord blood	blood
28	chr6:37598800-37606400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:37598800-37606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:37599000-37605800	Weak transcription	A549	lung

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