Variant report

Variant	rs17139327
Chromosome Location	chr7:7937356-7937357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7936554..7939221-chr7:8008179..8010269,3	MCF-7	breast:
2	chr7:7932645..7934651-chr7:7935237..7938092,2	K562	blood:
3	chr7:7935831..7938842-chr7:8008024..8010603,3	MCF-7	breast:
4	chr7:7935711..7938261-chr7:7941744..7943349,2	K562	blood:

Variant related genes	Relation type
ENSG00000233108	Chromatin interaction
ENSG00000106415	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12673370	0.89[ASN][1000 genomes]
rs1541515	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17139263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463745	0.86[CHB][hapmap]
rs7804964	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	84 gene(s)	inside rSNPs	diseases
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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 target site	59 gene(s)	inside rSNPs	diseases
3	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1027770	chr7:7797431-7957507	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538722	chr7:7797431-7957507	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv464304	chr7:7913819-7970560	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv606046	chr7:7913819-7970560	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv606047	chr7:7929851-7946400	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17139327	EIF2AK1	cis	parietal	SCAN
rs17139327	COL28A1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7897200-7942400	Weak transcription	Aorta	Aorta
2	chr7:7909600-7942400	Weak transcription	Left Ventricle	heart
3	chr7:7913200-7942400	Weak transcription	Primary T cells from cord blood	blood
4	chr7:7915800-7943000	Weak transcription	Gastric	stomach
5	chr7:7928600-7942400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:7930200-7951000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:7932200-7937600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:7934600-7939000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr7:7934800-7937400	Enhancers	HSMM	muscle
10	chr7:7935000-7942400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:7935000-7951600	Weak transcription	Pancreas	Pancrea
12	chr7:7935400-7952600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:7935600-7949000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:7936200-7938000	Enhancers	Fetal Heart	heart
15	chr7:7936400-7937800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:7936400-7938000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:7936600-7937800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:7936600-7938000	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr7:7936600-7938800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr7:7936600-7939000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr7:7936800-7937400	Enhancers	HMEC	breast
22	chr7:7936800-7937400	Enhancers	NHEK	skin
23	chr7:7936800-7938000	Enhancers	NHDF-Ad	bronchial
24	chr7:7936800-7938800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr7:7936800-7938800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr7:7937000-7937400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:7937000-7937400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr7:7937000-7937400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:7937000-7938600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:7937200-7937400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr7:7937200-7938600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:7937200-7938800	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links