Variant report

Variant	rs42941
Chromosome Location	chr22:30970972-30970973
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:30970774-30973067	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr22:30970970-30972658	K562	blood:	n/a	n/a
3	CEBPB	chr22:30970892-30971066	HepG2	liver:	n/a	chr22:30970977-30970988
4	POLR2A	chr22:30970918-30971197	GM12878	blood:	n/a	n/a
5	POLR2A	chr22:30970702-30971836	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr22:30970965-30972203	GM12878	blood:	n/a	n/a
7	POLR2A	chr22:30970772-30972180	GM12891	blood:	n/a	n/a
8	SIN3AK20	chr22:30970971-30971290	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr22:30970841-30971980	GM12892	blood:	n/a	n/a
10	POLR2A	chr22:30969819-30972027	HepG2	liver:	n/a	n/a
11	POLR2A	chr22:30970672-30972299	GM12892	blood:	n/a	n/a
12	POLR2A	chr22:30970282-30971008	HepG2	liver:	n/a	n/a
13	ATF2	chr22:30970966-30971298	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTBP2	chr22:30970768-30971525	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr22:30970940-30971090	A549	lung:	n/a	n/a
16	POLR2A	chr22:30970792-30971352	HepG2	liver:	n/a	n/a
17	POLR2A	chr22:30970851-30972204	GM12892	blood:	n/a	n/a
18	POLR2A	chr22:30970745-30971392	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr22:30970912-30972354	HL-60	blood:	n/a	n/a
20	POLR2A	chr22:30970729-30972168	GM12878	blood:	n/a	n/a
21	POLR2A	chr22:30970953-30972323	HL-60	blood:	n/a	n/a
22	POLR2A	chr22:30970707-30972267	K562	blood:	n/a	n/a
23	POLR2A	chr22:30970689-30972410	GM12892	blood:	n/a	n/a
24	POLR2A	chr22:30970743-30971760	U87	brain:	n/a	n/a
25	MAZ	chr22:30970840-30971158	HepG2	liver:	n/a	n/a
26	SIN3A	chr22:30970734-30971484	H1-hESC	embryonic stem cell:	n/a	chr22:30971312-30971321
27	GABPA	chr22:30970714-30971016	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr22:30970664-30972633	GM12878	blood:	n/a	n/a
29	POLR2A	chr22:30970748-30972829	K562	blood:	n/a	n/a
30	POLR2A	chr22:30970686-30972107	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr22:30970945-30972268	GM12891	blood:	n/a	n/a
32	POLR2A	chr22:30970933-30972197	K562	blood:	n/a	n/a
33	POLR2A	chr22:30970709-30970985	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr22:30970880-30971442	Hela-S3	cervix:	n/a	n/a
35	CEBPB	chr22:30970880-30971080	K562	blood:	n/a	chr22:30970977-30970988
36	YY1	chr22:30970760-30970981	H1-hESC	embryonic stem cell:	n/a	chr22:30970803-30970812 chr22:30970806-30970815 chr22:30970803-30970814 chr22:30970804-30970818
37	POLR2A	chr22:30970897-30972117	GM12891	blood:	n/a	n/a
38	POLR2A	chr22:30970737-30971760	U87	brain:	n/a	n/a
39	CEBPB	chr22:30970820-30971144	H1-hESC	embryonic stem cell:	n/a	chr22:30970977-30970988

No.	Distal block	Cell Line	Cell type
1	chr22:30969461..30973158-chr22:30985013..30988022,5	MCF-7	breast:
2	chr22:30964660..30967632-chr22:30970789..30972723,2	MCF-7	breast:
3	chr22:30970968..30972609-chr22:30985302..30987086,2	K562	blood:
4	chr22:30964568..30966833-chr22:30970828..30972723,3	MCF-7	breast:
5	chr22:30968308..30971950-chr22:30982173..30985267,5	K562	blood:
6	chr22:30968228..30973884-chr22:30985019..30988219,5	MCF-7	breast:

Variant related genes	Relation type
GAL3ST1	TF binding region
ENSG00000100029	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16988790	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs42931	0.94[ASW][hapmap];0.88[CEU][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap]
rs42932	0.84[CEU][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs42938	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42939	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5997685	0.97[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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv588887	chr22:30953521-30995356	Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv3377293	chr22:30969852-30971750	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs42941	KIAA1671	cis	parietal	SCAN
rs42941	MTMR3	cis	cerebellum	SCAN
rs42941	SLC35E4	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30964400-30979600	Weak transcription	K562	blood
2	chr22:30965600-30971000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr22:30967000-30971600	Enhancers	Placenta	Placenta
4	chr22:30967800-30971200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr22:30968000-30971600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:30968400-30971200	Weak transcription	Dnd41	blood
7	chr22:30968600-30971200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr22:30968800-30971000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr22:30968800-30971200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr22:30968800-30971200	Weak transcription	HMEC	breast
11	chr22:30968800-30971800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr22:30969000-30971000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr22:30969000-30971200	Enhancers	Lung	lung
14	chr22:30969000-30971400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr22:30969000-30971600	Active TSS	Rectal Smooth Muscle	rectum
16	chr22:30969400-30971000	Active TSS	Brain Anterior Caudate	brain
17	chr22:30969400-30971000	Weak transcription	GM12878-XiMat	blood
18	chr22:30969400-30971000	Enhancers	HSMM	muscle
19	chr22:30969600-30971000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr22:30969600-30971000	Active TSS	Brain Angular Gyrus	brain
21	chr22:30969600-30971000	Active TSS	Brain Cingulate Gyrus	brain
22	chr22:30969600-30971000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr22:30969600-30971200	Active TSS	Brain Substantia Nigra	brain
24	chr22:30969800-30971000	Active TSS	Brain Hippocampus Middle	brain
25	chr22:30969800-30971000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr22:30970000-30971000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr22:30970000-30971000	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr22:30970000-30971000	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr22:30970000-30971000	Active TSS	Duodenum Mucosa	Duodenum
30	chr22:30970000-30971000	Active TSS	A549	lung
31	chr22:30970000-30971400	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr22:30970000-30971400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr22:30970000-30971400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr22:30970000-30971400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr22:30970000-30971600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr22:30970000-30977200	Weak transcription	Hela-S3	cervix
37	chr22:30970200-30971000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr22:30970200-30971000	Active TSS	H1 Cell Line	embryonic stem cell
39	chr22:30970200-30971000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr22:30970200-30971000	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr22:30970200-30971000	Weak transcription	Spleen	Spleen
42	chr22:30970200-30971000	Active TSS	HepG2	liver
43	chr22:30970200-30971000	Weak transcription	HSMMtube	muscle
44	chr22:30970200-30971200	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr22:30970200-30971200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr22:30970200-30971600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
47	chr22:30970200-30971600	Enhancers	Psoas Muscle	Psoas
48	chr22:30970200-30971600	Enhancers	NHDF-Ad	bronchial
49	chr22:30970400-30971000	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr22:30970400-30971000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links