Variant report

Variant	rs9491973
Chromosome Location	chr6:128821006-128821007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr6:128820472-128821053	A549	lung:	n/a	n/a
2	MYBL2	chr6:128819946-128821191	HepG2	liver:	n/a	n/a
3	STAT3	chr6:128820547-128821046	MCF10A-Er-Src	breast:	n/a	n/a
4	FOSL2	chr6:128820427-128821071	A549	lung:	n/a	n/a
5	ARID3A	chr6:128819996-128821599	HepG2	liver:	n/a	n/a
6	SP1	chr6:128820424-128821113	A549	lung:	n/a	n/a
7	NFIC	chr6:128819836-128821251	HepG2	liver:	n/a	n/a
8	E2F4	chr6:128820551-128821221	MCF10A-Er-Src	breast:	n/a	n/a
9	GATA3	chr6:128820468-128821064	A549	lung:	n/a	n/a
10	TCF12	chr6:128820378-128821608	A549	lung:	n/a	n/a
11	TEAD4	chr6:128820301-128821188	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:128819294..128822394-chr6:128840492..128843286,6	MCF-7	breast:
2	chr6:128818473..128821360-chr6:128825336..128827931,3	MCF-7	breast:
3	chr6:128817983..128822479-chr6:128839649..128843314,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224733	TF binding region
ENSG00000152894	Chromatin interaction
ENSG00000227112	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12333125	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196432	0.83[YRI][hapmap]
rs1417900	0.95[CEU][hapmap];0.83[GIH][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053280	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055907	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35801729	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569535	1.00[CHD][hapmap]
rs6921395	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923822	1.00[CHD][hapmap]
rs7751265	1.00[CHD][hapmap]
rs9321120	1.00[ASN][1000 genomes]
rs9482889	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491960	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491965	0.86[CEU][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs9491976	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492001	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9491973	AKAP7	cis	parietal	SCAN
rs9491973	MOXD1	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128797400-128822000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:128808800-128830800	Weak transcription	Lung	lung
3	chr6:128813000-128828600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:128813400-128825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:128814000-128825200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:128814200-128821200	Weak transcription	Osteobl	bone
7	chr6:128814200-128821800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:128814200-128822200	Weak transcription	Fetal Stomach	stomach
9	chr6:128814200-128824800	Weak transcription	Right Ventricle	heart
10	chr6:128815000-128821200	Weak transcription	NHLF	lung
11	chr6:128815200-128833800	Enhancers	Fetal Intestine Large	intestine
12	chr6:128815600-128822600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:128815800-128822800	Weak transcription	Fetal Thymus	thymus
14	chr6:128816400-128825600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:128816800-128826600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:128817200-128822000	Weak transcription	Left Ventricle	heart
17	chr6:128817200-128828600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:128817200-128839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:128817200-128839800	Weak transcription	Aorta	Aorta
20	chr6:128818800-128821800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr6:128818800-128822000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:128819000-128822400	Enhancers	Fetal Heart	heart
23	chr6:128819200-128821200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr6:128819200-128821800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:128819200-128823400	Enhancers	Fetal Lung	lung
26	chr6:128819600-128821200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:128819600-128821200	Weak transcription	NH-A	brain
28	chr6:128819600-128821400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:128819600-128821600	Enhancers	Brain Substantia Nigra	brain
30	chr6:128819600-128824000	Weak transcription	Pancreas	Pancrea
31	chr6:128819600-128824600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:128819600-128825200	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:128819600-128827600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:128819800-128821200	Weak transcription	Colonic Mucosa	Colon
35	chr6:128819800-128821200	Weak transcription	Gastric	stomach
36	chr6:128819800-128821800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr6:128819800-128822000	Weak transcription	Fetal Brain Male	brain
38	chr6:128819800-128824800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:128819800-128824800	Weak transcription	Ovary	ovary
40	chr6:128819800-128825200	Weak transcription	Small Intestine	intestine
41	chr6:128819800-128825400	Weak transcription	Psoas Muscle	Psoas
42	chr6:128819800-128825600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:128819800-128825600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:128819800-128825600	Weak transcription	Right Atrium	heart
45	chr6:128819800-128826600	Weak transcription	Brain Angular Gyrus	brain
46	chr6:128819800-128828600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:128819800-128828600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:128820200-128821400	Flanking Active TSS	HepG2	liver
49	chr6:128820200-128822200	Enhancers	Stomach Mucosa	stomach
50	chr6:128820400-128821200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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