Variant report

Variant	rs16990370
Chromosome Location	chr22:32781587-32781588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:32781264-32781850	GM12892	blood:	n/a	n/a
2	POLR2A	chr22:32781156-32782015	GM12891	blood:	n/a	n/a
3	POLR2A	chr22:32780745-32782812	K562	blood:	n/a	n/a
4	POLR2A	chr22:32780687-32782251	GM12891	blood:	n/a	n/a
5	POLR2A	chr22:32781525-32781826	GM12891	blood:	n/a	n/a
6	POLR2A	chr22:32781193-32781674	HL-60	blood:	n/a	n/a
7	POLR2A	chr22:32781349-32782753	HepG2	liver:	n/a	n/a
8	POLR2A	chr22:32781104-32782956	GM12892	blood:	n/a	n/a
9	POLR2A	chr22:32781576-32781716	MCF-7	breast:	n/a	n/a
10	POLR2A	chr22:32781198-32781780	K562	blood:	n/a	n/a
11	POLR2A	chr22:32781188-32782796	GM12891	blood:	n/a	n/a
12	POLR2A	chr22:32781188-32781685	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr22:32781242-32782808	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr22:32780754-32781760	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr22:32781550-32781712	GM12878	blood:	n/a	n/a
16	POLR2A	chr22:32781260-32781874	HepG2	liver:	n/a	n/a
17	POLR2A	chr22:32781541-32781749	GM12878	blood:	n/a	n/a
18	POLR2A	chr22:32781481-32781864	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr22:32781145-32781843	GM12878	blood:	n/a	n/a
20	POLR2A	chr22:32781145-32781873	GM12892	blood:	n/a	n/a
21	POLR2A	chr22:32781285-32782475	GM12891	blood:	n/a	n/a
22	POLR2A	chr22:32780932-32781953	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:31829733-31836635..22:32764253-32784733	K562	blood:
2	22:31936958-31958600..22:32764253-32784733	K562	blood:
3	22:32529813-32538538..22:32764253-32784733	H1-hESC	embryonic stem cell:	embryo
4	22:32513817-32522138..22:32764253-32784733	H1-hESC	embryonic stem cell:	embryo
5	22:32360288-32405313..22:32764253-32784733	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFPL3-1	chr22:32781443-32781618	ENSG00000241954.1

No data

Variant related genes	Relation type
ENSG00000232218	TF binding region
RFPL3S	TF binding region
ENSG00000230866	Chromatin interaction
ENSG00000234479	Chromatin interaction
ENSG00000240647	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000214093	Chromatin interaction
ENSG00000239674	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11912086	0.82[AFR][1000 genomes]
rs11912716	0.83[AFR][1000 genomes]
rs11914186	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17690161	1.00[CEU][hapmap]
rs2072816	0.84[YRI][hapmap]
rs59857514	0.82[AFR][1000 genomes]
rs60043294	0.94[AFR][1000 genomes]
rs61138259	0.94[AFR][1000 genomes]
rs7286662	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7287940	0.94[AFR][1000 genomes]
rs7289771	0.82[AFR][1000 genomes]

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	esv2422247	chr22:32486448-32788258	Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers 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	38 gene(s)	inside rSNPs	diseases
5	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32755800-32781600	Weak transcription	Ovary	ovary
2	chr22:32762800-32788200	Weak transcription	Psoas Muscle	Psoas
3	chr22:32772800-32781600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr22:32773800-32781600	Weak transcription	Esophagus	oesophagus
5	chr22:32774000-32782000	Weak transcription	Primary B cells from cord blood	blood
6	chr22:32775000-32783400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:32775200-32782000	Weak transcription	HMEC	breast
8	chr22:32775200-32782200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr22:32775200-32782200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr22:32775200-32782200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr22:32775200-32782400	Weak transcription	Brain Hippocampus Middle	brain
12	chr22:32775200-32782600	Weak transcription	Right Ventricle	heart
13	chr22:32775200-32783200	Weak transcription	HepG2	liver
14	chr22:32775400-32781600	Weak transcription	Brain Angular Gyrus	brain
15	chr22:32775400-32781600	Weak transcription	Brain Substantia Nigra	brain
16	chr22:32775400-32781600	Weak transcription	Spleen	Spleen
17	chr22:32775400-32783000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr22:32775400-32783400	Weak transcription	K562	blood
19	chr22:32775600-32783400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr22:32777200-32793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr22:32778000-32781600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr22:32778000-32781800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr22:32778600-32781800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr22:32778600-32782200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr22:32779400-32781600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr22:32779400-32781600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr22:32779400-32782200	Weak transcription	HUVEC	blood vessel
28	chr22:32779600-32781600	Weak transcription	Pancreas	Pancrea
29	chr22:32779800-32781600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr22:32779800-32783400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr22:32780000-32781600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr22:32780000-32781600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr22:32780000-32781600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr22:32780000-32781600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr22:32780000-32781600	Weak transcription	Aorta	Aorta
36	chr22:32780000-32782600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr22:32780000-32783200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr22:32780000-32783400	Weak transcription	HSMMtube	muscle
39	chr22:32780000-32790400	Weak transcription	Fetal Brain Male	brain
40	chr22:32780200-32781800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr22:32780200-32781800	Weak transcription	Fetal Brain Female	brain
42	chr22:32780200-32783400	Weak transcription	HSMM	muscle
43	chr22:32780400-32782000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr22:32780600-32782200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr22:32780600-32783400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr22:32780800-32782400	Weak transcription	Colonic Mucosa	Colon
47	chr22:32780800-32783200	Weak transcription	Small Intestine	intestine
48	chr22:32780800-32784200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr22:32780800-32789000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr22:32780800-32806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links