Variant report

Variant	rs74150559
Chromosome Location	chr1:226109804-226109805
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:226108694-226110229	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:226108799-226110815	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:226108816-226110681	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:226108978-226110162	Raji	blood:	n/a	n/a
5	POLR2A	chr1:226108745-226110855	K562	blood:	n/a	n/a
6	POLR2A	chr1:226109246-226110709	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr1:226108694-226113166	K562	blood:	n/a	n/a
8	POLR2A	chr1:226108930-226110705	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:226108389-226110845	K562	blood:	n/a	n/a
10	POLR2A	chr1:226108252-226113105	K562	blood:	n/a	n/a
11	POLR2A	chr1:226108662-226112566	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr1:226109769-226110085	A549	lung:	n/a	n/a
13	POLR2A	chr1:226108743-226109910	HL-60	blood:	n/a	n/a
14	POLR2A	chr1:226109498-226110616	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr1:226108269-226110812	K562	blood:	n/a	n/a
16	POLR2A	chr1:226108715-226110854	K562	blood:	n/a	n/a
17	POLR2A	chr1:226109784-226109964	A549	lung:	n/a	n/a
18	CTCF	chr1:226109760-226109910	GM12865	blood:	n/a	n/a
19	POLR2A	chr1:226108793-226110711	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:226108594-226112501	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr1:226103313-226112422	K562	blood:	n/a	n/a
22	POLR2A	chr1:226108439-226113183	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:226109389-226110008	A549	lung:	n/a	n/a
24	POLR2A	chr1:226108770-226110782	K562	blood:	n/a	n/a
25	POLR2A	chr1:226107223-226113112	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226108702..226117785-chr1:226183554..226190529,14	K562	blood:
2	chr1:226066440..226072029-chr1:226106315..226113044,10	MCF-7	breast:
3	chr1:226067470..226074101-chr1:226108823..226116408,13	MCF-7	breast:
4	chr1:226063406..226070293-chr1:226107715..226112317,7	K562	blood:

No data

Variant related genes	Relation type
PYCR2	TF binding region
ENSG00000196187	Chromatin interaction
ENSG00000143751	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10915895	0.89[AMR][1000 genomes]
rs10915902	0.81[AMR][1000 genomes]
rs10915903	0.81[AMR][1000 genomes]
rs12071072	0.83[AFR][1000 genomes]
rs12071104	0.83[AFR][1000 genomes]
rs12078868	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080725	0.89[AMR][1000 genomes]
rs12092868	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094548	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35273824	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs35684337	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56035614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6700642	0.81[AMR][1000 genomes]
rs74150558	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150561	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' 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	39 gene(s)	inside rSNPs	diseases
5	esv3335650	chr1:226074720-226125458	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh 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	19 gene(s)	inside rSNPs	diseases
6	esv3369235	chr1:226075748-226127738	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv468216	chr1:226078915-226135132	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv549267	chr1:226078915-226135132	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription 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	19 gene(s)	inside rSNPs	diseases
9	nsv535314	chr1:226087226-226128261	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226100400-226110400	Weak transcription	Small Intestine	intestine
2	chr1:226101600-226110400	Strong transcription	Fetal Intestine Small	intestine
3	chr1:226102800-226111000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:226103400-226110200	Strong transcription	Thymus	Thymus
5	chr1:226103600-226110000	Strong transcription	Fetal Intestine Large	intestine
6	chr1:226103600-226111200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:226104600-226110200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:226104600-226110400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:226104600-226110800	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr1:226104800-226110400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:226105000-226110000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:226105200-226110400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:226105400-226110400	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr1:226105400-226110600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:226105800-226110000	Strong transcription	A549	lung
16	chr1:226105800-226110200	Strong transcription	HepG2	liver
17	chr1:226106000-226110000	Weak transcription	Hela-S3	cervix
18	chr1:226106000-226110400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:226106000-226110600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:226106000-226111000	Weak transcription	HSMMtube	muscle
21	chr1:226106200-226111200	Weak transcription	Aorta	Aorta
22	chr1:226106600-226110400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:226106800-226110600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:226107000-226110000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:226107200-226110000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:226107200-226110000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:226107200-226110000	Genic enhancers	Brain Germinal Matrix	brain
28	chr1:226107200-226110200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:226107200-226110400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:226107200-226110400	Genic enhancers	GM12878-XiMat	blood
31	chr1:226107200-226110600	Genic enhancers	Primary T cells from cord blood	blood
32	chr1:226107200-226110600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:226107200-226110800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:226107200-226111000	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr1:226107400-226110200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:226107400-226111000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:226107600-226110000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:226107800-226110200	Strong transcription	Primary B cells from cord blood	blood
39	chr1:226107800-226110800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:226108000-226110000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:226108000-226110000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:226108000-226110000	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:226108000-226110000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:226108000-226110000	Weak transcription	NHDF-Ad	bronchial
45	chr1:226108000-226110200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:226108000-226110200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:226108000-226110400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr1:226108000-226110400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:226108000-226110400	Weak transcription	Fetal Heart	heart
50	chr1:226108000-226110400	Strong transcription	HSMM	muscle

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