Variant report

Variant	rs757031
Chromosome Location	chr7:111393626-111393627
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:111392617..111395439-chr7:112089708..112091981,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10246451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10275090	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11971917	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705797	0.85[ASN][1000 genomes]
rs17545234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2078984	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2097712	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3757648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3779458	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3801792	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4416770	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4730498	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6950977	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7803753	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs867915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9641471	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9691349	1.00[CHB][hapmap];0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2764041	chr7:110918713-111395390	Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv608196	chr7:111073710-111794368	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv932103	chr7:111092431-111412049	Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv869375	chr7:111105151-111470811	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
5	nsv608215	chr7:111183610-111533520	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS 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	14 gene(s)	inside rSNPs	diseases
6	nsv1021527	chr7:111194596-111851619	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539086	chr7:111194596-111851619	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1028740	chr7:111227747-111679401	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1015267	chr7:111303294-111714771	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv539087	chr7:111303294-111714771	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
11	nsv539088	chr7:111333899-111722341	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv531435	chr7:111333900-111926292	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv491934	chr7:111333900-111975504	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1034375	chr7:111337109-111459099	Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs757031	PNLDC1	trans	lymphoblastoid	seeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:111363000-111418000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:111366800-111394200	Weak transcription	Gastric	stomach
3	chr7:111367400-111401600	Weak transcription	Colonic Mucosa	Colon
4	chr7:111373600-111414000	Weak transcription	Right Ventricle	heart
5	chr7:111375800-111394200	Weak transcription	Fetal Heart	heart
6	chr7:111376000-111399600	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:111376600-111397000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:111376600-111398200	Weak transcription	A549	lung
9	chr7:111377000-111396800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:111377000-111396800	Weak transcription	HMEC	breast
11	chr7:111379600-111398000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr7:111379600-111433600	Weak transcription	Esophagus	oesophagus
13	chr7:111379800-111398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:111380000-111396600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:111383800-111396600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:111383800-111396600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:111383800-111396600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:111383800-111396600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:111383800-111396800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:111383800-111396800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:111383800-111400200	Weak transcription	Aorta	Aorta
22	chr7:111384000-111396800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:111384400-111393800	Weak transcription	Brain Germinal Matrix	brain
24	chr7:111384400-111409000	Weak transcription	Fetal Stomach	stomach
25	chr7:111384600-111394600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:111384600-111396400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:111384600-111396400	Weak transcription	Lung	lung
28	chr7:111384600-111396800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:111384600-111396800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:111384800-111393800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:111385000-111396400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:111385200-111394600	Weak transcription	Left Ventricle	heart
33	chr7:111385200-111396400	Weak transcription	NHLF	lung
34	chr7:111385200-111396600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:111385200-111396600	Weak transcription	Osteobl	bone
36	chr7:111385200-111397000	Weak transcription	NH-A	brain
37	chr7:111385200-111399400	Weak transcription	NHEK	skin
38	chr7:111385400-111393800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:111385400-111396800	Weak transcription	NHDF-Ad	bronchial
40	chr7:111385400-111398000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:111385600-111396600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:111385600-111403600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr7:111386200-111394200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:111387400-111397000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:111387400-111398000	Weak transcription	Ovary	ovary
46	chr7:111388000-111396400	Weak transcription	Adipose Nuclei	Adipose
47	chr7:111388200-111393800	Weak transcription	Brain Hippocampus Middle	brain
48	chr7:111389200-111394200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:111389200-111396600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:111389200-111416800	Weak transcription	Placenta	Placenta

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