Variant report

Variant	rs1046332
Chromosome Location	chr1:149817508-149817509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:149800421-149817942	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:149814988-149821817	K562	blood:	n/a	n/a
3	BCL3	chr1:149817251-149817746	K562	blood:	n/a	n/a
4	BCLAF1	chr1:149816098-149817560	K562	blood:	n/a	n/a
5	CHD2	chr1:149816885-149817554	H1-hESC	embryonic stem cell:	n/a	n/a
6	PML	chr1:149816915-149817647	MCF-7	breast:	n/a	n/a
7	TBL1XR1	chr1:149817431-149817675	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:149814991-149821919	K562	blood:	n/a	n/a
9	CHD2	chr1:149816910-149817914	K562	blood:	n/a	n/a
10	POLR2A	chr1:149816393-149817543	PANC-1	pancreas:	n/a	n/a
11	ZNF143	chr1:149817461-149817629	K562	blood:	n/a	n/a
12	MAFK	chr1:149816935-149817548	H1-hESC	embryonic stem cell:	n/a	n/a
13	TAF7	chr1:149814973-149817543	H1-hESC	embryonic stem cell:	n/a	n/a
14	ARID3A	chr1:149817086-149817880	K562	blood:	n/a	n/a
15	CHD1	chr1:149815008-149817854	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAFF	chr1:149816984-149817849	K562	blood:	n/a	n/a
17	POLR2A	chr1:149814975-149819632	K562	blood:	n/a	n/a
18	POLR2A	chr1:149815112-149817954	HepG2	liver:	n/a	n/a
19	SIN3AK20	chr1:149817425-149817787	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:149815719..149822339-chr1:149907112..149913890,13	MCF-7	breast:
2	chr1:149813687..149823244-chr1:149851297..149861525,76	MCF-7	breast:
3	chr1:149813928..149823076-chr1:149854513..149862208,33	K562	blood:
4	chr1:149815410..149817794-chr1:149900163..149901806,2	K562	blood:
5	chr1:149815281..149817675-chr1:149980545..149983333,2	K562	blood:
6	chr1:149780184..149786348-chr1:149813638..149819174,10	MCF-7	breast:
7	chr1:149814002..149823234-chr1:149906555..149912579,18	MCF-7	breast:
8	chr1:149813697..149823354-chr1:149851773..149862006,115	MCF-7	breast:
9	chr1:149813771..149823366-chr1:149853740..149862208,36	K562	blood:
10	chr1:149817384..149819786-chr20:62610285..62612277,2	MCF-7	breast:
11	chr1:149815885..149817611-chr1:150124360..150125922,2	K562	blood:
12	chr1:149813582..149820276-chr1:149898052..149903861,9	MCF-7	breast:
13	chr1:149816826..149819259-chr8:99056422..99059164,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIST2H2AA3-1	chr1:149816065-149820591	ENSG00000261716.1
2	lnc-HIST2H2AA4-1	chr1:149817383-149818053	ENSG00000272993.1

No data

Variant related genes	Relation type
HIST2H3C	TF binding region
HIST2H2AA3	TF binding region
ENSG00000184260	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000156482	Chromatin interaction
ENSG00000014914	Chromatin interaction
ENSG00000203814	Chromatin interaction
ENSG00000130590	Chromatin interaction
ENSG00000143368	Chromatin interaction
ENSG00000242663	Chromatin interaction
ENSG00000183598	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000163113	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1044808	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10494261	1.00[GIH][hapmap]
rs10494363	1.00[GIH][hapmap]
rs11205308	1.00[GIH][hapmap]
rs11577346	1.00[AFR][1000 genomes]
rs11584354	1.00[AFR][1000 genomes]
rs12060830	1.00[GIH][hapmap];0.82[MEX][hapmap]
rs12062387	0.90[EUR][1000 genomes]
rs12078573	0.81[CEU][hapmap];1.00[GIH][hapmap];0.81[EUR][1000 genomes]
rs1349532	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1376675	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1376676	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs1451641	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs15931	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16835135	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs16836630	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs17643644	0.81[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs1804775	0.81[EUR][1000 genomes]
rs2474478	0.93[AMR][1000 genomes]
rs28560140	1.00[AFR][1000 genomes]
rs3106121	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes]
rs41264630	0.83[EUR][1000 genomes]
rs45548131	0.82[EUR][1000 genomes]
rs55633017	0.90[EUR][1000 genomes]
rs55664407	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55705001	0.82[EUR][1000 genomes]
rs55885412	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56119131	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56139516	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56212907	1.00[AFR][1000 genomes]
rs56229803	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56265028	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61355654	0.90[EUR][1000 genomes]
rs68144650	0.82[EUR][1000 genomes]
rs72692803	0.83[EUR][1000 genomes]
rs72692804	0.82[EUR][1000 genomes]
rs72692805	0.82[EUR][1000 genomes]
rs72692807	0.82[EUR][1000 genomes]
rs72692808	0.82[EUR][1000 genomes]
rs72692810	0.82[EUR][1000 genomes]
rs72692811	0.82[EUR][1000 genomes]
rs72692812	0.82[EUR][1000 genomes]
rs72692813	0.81[EUR][1000 genomes]
rs72692814	0.81[EUR][1000 genomes]
rs72692816	0.81[EUR][1000 genomes]
rs72692818	0.81[EUR][1000 genomes]
rs72692819	0.81[EUR][1000 genomes]
rs72692873	1.00[AFR][1000 genomes]
rs72692886	1.00[AFR][1000 genomes]
rs72692893	1.00[AFR][1000 genomes]
rs72692898	1.00[AFR][1000 genomes]
rs72692899	1.00[AFR][1000 genomes]
rs72692900	1.00[AFR][1000 genomes]
rs72694914	1.00[AFR][1000 genomes]
rs72694915	1.00[AFR][1000 genomes]
rs72694923	1.00[AFR][1000 genomes]
rs72694926	1.00[AFR][1000 genomes]
rs72708145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72708148	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72708149	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72708150	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72708151	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72708152	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72708153	0.90[EUR][1000 genomes]
rs72708157	0.90[EUR][1000 genomes]
rs72708158	0.87[EUR][1000 genomes]
rs72708162	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7524797	0.87[EUR][1000 genomes]
rs7544531	0.90[CEU][hapmap];1.00[GIH][hapmap]

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	nsv432820	chr1:148921404-149920927	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	784 gene(s)	inside rSNPs	diseases
2	esv1806395	chr1:149015282-149849940	Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	425 gene(s)	inside rSNPs	diseases
3	esv1831586	chr1:149036382-149849940	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	425 gene(s)	inside rSNPs	diseases
4	nsv831503	chr1:149640643-149820841	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv469694	chr1:149688852-149836280	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482790	chr1:149688852-149836280	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv831525	chr1:149701537-149878033	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
8	nsv547843	chr1:149798606-149818466	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1046332	POLR3GL	cis	cerebellum	SCAN
rs1046332	OTUD7B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149815000-149817600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:149815000-149817600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:149815000-149817800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr1:149815000-149817800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:149815000-149818000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr1:149815200-149817600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr1:149815200-149817800	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr1:149815400-149820400	Weak transcription	Gastric	stomach
9	chr1:149815400-149821200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:149815400-149821600	Weak transcription	Lung	lung
11	chr1:149815600-149817600	Enhancers	Stomach Mucosa	stomach
12	chr1:149815600-149819200	Weak transcription	Colonic Mucosa	Colon
13	chr1:149815600-149820000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:149815600-149820000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:149815600-149820200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:149815600-149820400	Weak transcription	Psoas Muscle	Psoas
17	chr1:149815600-149821000	Weak transcription	Left Ventricle	heart
18	chr1:149815600-149821600	Weak transcription	Esophagus	oesophagus
19	chr1:149815800-149817600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:149815800-149817600	Enhancers	Brain Hippocampus Middle	brain
21	chr1:149815800-149819000	Enhancers	Placenta Amnion	Placenta Amnion
22	chr1:149815800-149820000	Weak transcription	HSMMtube	muscle
23	chr1:149815800-149820600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:149815800-149820800	Weak transcription	Right Atrium	heart
25	chr1:149816000-149820000	Weak transcription	Fetal Brain Female	brain
26	chr1:149816000-149820000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:149816000-149820200	Weak transcription	Adipose Nuclei	Adipose
28	chr1:149816000-149820400	Weak transcription	Right Ventricle	heart
29	chr1:149816200-149817600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:149816200-149817600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr1:149816200-149817800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr1:149816200-149817800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:149816200-149817800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr1:149816200-149818600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr1:149816400-149817600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
36	chr1:149816400-149817600	Transcr. at gene 5' and 3'	A549	lung
37	chr1:149816400-149818000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr1:149816400-149818000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:149816400-149819000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:149816400-149820000	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr1:149816400-149821200	Transcr. at gene 5' and 3'	K562	blood
42	chr1:149816600-149817800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:149816600-149817800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr1:149816600-149818000	Enhancers	NHEK	skin
45	chr1:149816600-149818600	Weak transcription	HSMM	muscle
46	chr1:149816600-149820000	Enhancers	HepG2	liver
47	chr1:149816800-149817600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:149816800-149818200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:149816800-149819000	Strong transcription	Placenta	Placenta
50	chr1:149816800-149819800	Weak transcription	Muscle Satellite Cultured Cells	--

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