Variant report

Variant	rs9821797
Chromosome Location	chr3:48718253-48718254
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48717899-48718429	K562	blood:	n/a	n/a
2	POLR2A	chr3:48718115-48718367	K562	blood:	n/a	n/a
3	POLR2A	chr3:48718144-48718412	K562	blood:	n/a	n/a
4	POLR2A	chr3:48718058-48718254	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:48718182-48718382	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:48718247-48718504	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:48716844-48718670	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:48718209-48718331	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48593859..48595612-chr3:48717016..48718760,2	MCF-7	breast:
2	chr3:48717071..48719987-chr3:48721738..48723845,3	MCF-7	breast:
3	chr3:48709842..48711551-chr3:48717118..48719830,2	MCF-7	breast:
4	chr3:48699299..48703873-chr3:48715927..48726939,20	MCF-7	breast:
5	chr3:48717662..48719232-chr3:48721596..48723446,2	MCF-7	breast:
6	chr3:48716233..48718830-chr3:48753340..48756269,2	K562	blood:

No data

Variant related genes	Relation type
NCKIPSD	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000271973	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10470687	1.00[JPT][hapmap]
rs11557629	0.85[EUR][1000 genomes]
rs11706203	0.82[EUR][1000 genomes]
rs11706983	0.85[EUR][1000 genomes]
rs11719291	0.85[EUR][1000 genomes]
rs12107252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12107418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12715429	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060933	1.00[JPT][hapmap]
rs13063223	0.82[EUR][1000 genomes]
rs13063312	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13070798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076269	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090013	0.85[EUR][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13094578	0.82[JPT][hapmap]
rs13096357	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13316551	0.82[EUR][1000 genomes]
rs13319651	1.00[JPT][hapmap]
rs13324119	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324142	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13434258	0.85[EUR][1000 genomes]
rs17080319	0.85[EUR][1000 genomes]
rs2006871	1.00[JPT][hapmap]
rs2276850	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2276852	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286651	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286652	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2310996	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2310997	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28452701	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2854394	1.00[JPT][hapmap]
rs28567949	0.85[EUR][1000 genomes]
rs28657585	0.83[EUR][1000 genomes]
rs34096717	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34153629	0.85[EUR][1000 genomes]
rs34368826	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34577723	0.83[EUR][1000 genomes]
rs34638686	0.80[EUR][1000 genomes]
rs35064573	0.85[EUR][1000 genomes]
rs3733086	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821875	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821876	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57334642	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768448	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773261	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6781283	1.00[JPT][hapmap]
rs6792156	1.00[JPT][hapmap]
rs6792525	1.00[JPT][hapmap]
rs68042649	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806059	1.00[JPT][hapmap]
rs73078362	0.82[EUR][1000 genomes]
rs740787	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631574	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9809222	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810549	1.00[JPT][hapmap]
rs9811027	0.85[EUR][1000 genomes]
rs9811318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812977	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9830581	1.00[JPT][hapmap]
rs9836462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837687	1.00[JPT][hapmap]
rs9841602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843316	1.00[JPT][hapmap]
rs9850102	1.00[JPT][hapmap]
rs9854034	0.82[EUR][1000 genomes]
rs9868809	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9869698	1.00[JPT][hapmap]
rs9871180	1.00[JPT][hapmap]
rs9873726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877542	0.82[EUR][1000 genomes]
rs9877685	0.82[EUR][1000 genomes]
rs9878063	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9878950	1.00[JPT][hapmap]
rs9882549	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	esv3362881	chr3:48715948-48720546	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
8	nsv590248	chr3:48716993-48727636	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9821797	WDR6	cis	Esophagus Mucosa	GTEx
rs9821797	WDR6	cis	Adipose Subcutaneous	GTEx
rs9821797	WDR6	cis	lung	GTEx
rs9821797	WDR6	cis	Nerve Tibial	GTEx
rs9821797	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48701200-48721000	Weak transcription	Fetal Brain Male	brain
2	chr3:48701600-48720800	Weak transcription	Right Atrium	heart
3	chr3:48701600-48720800	Weak transcription	HUVEC	blood vessel
4	chr3:48701800-48721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:48702000-48721400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:48705800-48720600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:48707200-48721400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:48708200-48720200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:48708200-48720200	Strong transcription	Fetal Brain Female	brain
10	chr3:48708200-48720600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:48708200-48720600	Strong transcription	Fetal Intestine Small	intestine
12	chr3:48708200-48720600	Strong transcription	Fetal Stomach	stomach
13	chr3:48708200-48721000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:48708400-48720400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:48708400-48720400	Strong transcription	Brain Germinal Matrix	brain
16	chr3:48708400-48720400	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr3:48708400-48720800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:48708400-48721000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:48708600-48720600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:48708800-48720600	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr3:48709000-48721600	Weak transcription	Psoas Muscle	Psoas
22	chr3:48709200-48720200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr3:48710400-48719800	Strong transcription	Brain Cingulate Gyrus	brain
24	chr3:48710400-48721200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:48710600-48720200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:48711000-48720200	Strong transcription	Left Ventricle	heart
27	chr3:48711000-48720400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr3:48711200-48720000	Strong transcription	Liver	Liver
29	chr3:48711200-48720000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:48711400-48719200	Strong transcription	Brain Angular Gyrus	brain
31	chr3:48711400-48720000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:48711400-48720000	Strong transcription	Aorta	Aorta
33	chr3:48711400-48720000	Strong transcription	Brain Substantia Nigra	brain
34	chr3:48711400-48720000	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:48711400-48720000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr3:48711400-48720200	Strong transcription	Placenta	Placenta
37	chr3:48711400-48720400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr3:48711400-48720400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:48711400-48720400	Strong transcription	NHEK	skin
40	chr3:48711400-48720600	Strong transcription	Fetal Intestine Large	intestine
41	chr3:48711400-48721200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:48711600-48720400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:48711600-48720400	Strong transcription	Brain Hippocampus Middle	brain
44	chr3:48711600-48720600	Strong transcription	Adipose Nuclei	Adipose
45	chr3:48711600-48720600	Strong transcription	Brain Anterior Caudate	brain
46	chr3:48711600-48720600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:48711600-48720800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:48711800-48720200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:48711800-48720400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:48711800-48720400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links