Variant report

Variant	rs2902810
Chromosome Location	chr1:151026815-151026816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151025787-151026997	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:151026652-151027052	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:151019747-151029675	K562	blood:	n/a	n/a
4	POLR2A	chr1:151025849-151026996	K562	blood:	n/a	n/a
5	POLR2A	chr1:151021765-151027201	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:151023510-151029710	K562	blood:	n/a	n/a
7	POLR2A	chr1:151026003-151027159	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:151021742-151027117	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:151026478-151027051	K562	blood:	n/a	n/a
10	POLR2A	chr1:151026390-151027020	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr1:151026765-151026977	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:151026611-151028365	K562	blood:	n/a	n/a
13	POLR2A	chr1:151026635-151027014	GM12891	blood:	n/a	n/a
14	POLR2A	chr1:151021903-151029745	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:151021764-151027124	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:151026583-151027059	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:151026720-151026948	A549	lung:	n/a	n/a
18	POLR2A	chr1:151026046-151027282	K562	blood:	n/a	n/a
19	POLR2A	chr1:151025973-151027104	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:151026339-151027106	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr1:151026131-151027119	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:151026747-151027249	U87	brain:	n/a	n/a
23	POLR2A	chr1:151026808-151026958	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151005028..151012583-chr1:151026392..151034442,13	K562	blood:
2	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:

No data

Variant related genes	Relation type
MLLT11	TF binding region
ENSG00000163141	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000143409	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10788798	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10788799	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11204777	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11204778	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11204780	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12039542	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12117163	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1524773	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1969442	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2140709	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2864700	0.89[JPT][hapmap]
rs35550545	0.94[ASN][1000 genomes]
rs3738481	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3806386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806387	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4357530	0.83[CHD][hapmap]
rs4970939	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4970941	0.88[CHD][hapmap]
rs4970990	0.92[ASN][1000 genomes]
rs4970993	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4970998	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs4971005	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap]
rs4971007	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap]
rs4971008	0.94[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap]
rs6587552	0.81[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6587553	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6657593	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6668894	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6676190	0.83[CHD][hapmap]
rs6694158	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7366148	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532312	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs7540258	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs7550434	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2902810	PRPF3	cis	parietal	SCAN
rs2902810	RPTN	cis	cerebellum	SCAN
rs2902810	MRPS21	cis	cerebellum	SCAN
rs2902810	BNIPL	cis	Thyroid	GTEx
rs2902810	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs2902810	BNIPL	cis	lung	GTEx
rs2902810	BNIPL	cis	lymphoblastoid	seeQTL
rs2902810	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL
rs2902810	MRPS21	cis	parietal	SCAN
rs2902810	ARNT	cis	parietal	SCAN
rs2902810	CDC42SE1	cis	parietal	SCAN
rs2902810	CDC42SE1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151021200-151030400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:151021400-151028000	Weak transcription	Psoas Muscle	Psoas
3	chr1:151021400-151029000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:151021400-151030000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:151022000-151030000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:151022400-151027600	Strong transcription	Fetal Thymus	thymus
7	chr1:151022400-151027600	Strong transcription	GM12878-XiMat	blood
8	chr1:151022400-151028000	Strong transcription	Osteobl	bone
9	chr1:151022400-151028600	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr1:151022400-151029000	Strong transcription	NH-A	brain
11	chr1:151022400-151029200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:151022400-151029200	Strong transcription	NHDF-Ad	bronchial
13	chr1:151022400-151029400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:151022600-151027000	Strong transcription	HMEC	breast
15	chr1:151022600-151028000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr1:151022600-151028000	Strong transcription	Brain Substantia Nigra	brain
17	chr1:151022600-151028200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:151022600-151028600	Strong transcription	HSMM	muscle
19	chr1:151022600-151029200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:151022800-151027200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:151022800-151027800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:151022800-151027800	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:151022800-151028000	Strong transcription	Fetal Muscle Leg	muscle
24	chr1:151022800-151029400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:151022800-151029600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:151022800-151029600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:151023000-151027600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr1:151023000-151027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:151023000-151027800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:151023000-151027800	Strong transcription	Adipose Nuclei	Adipose
31	chr1:151023000-151027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:151023000-151027800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr1:151023000-151028000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:151023000-151028200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:151023000-151028600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:151023200-151027200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:151023200-151027400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:151023200-151027400	Strong transcription	Placenta	Placenta
39	chr1:151023200-151027800	Strong transcription	Liver	Liver
40	chr1:151023200-151028200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:151023200-151028200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:151023200-151028600	Strong transcription	HSMMtube	muscle
43	chr1:151023200-151029600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:151023400-151028200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:151023400-151029200	Strong transcription	Fetal Brain Female	brain
46	chr1:151023600-151027200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr1:151023600-151027600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:151023600-151027600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:151023600-151028200	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:151023600-151028200	Strong transcription	Rectal Smooth Muscle	rectum

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