Variant report

Variant	rs772173
Chromosome Location	chr2:97000396-97000397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr2:97000386-97000773	K562	blood:	n/a	n/a
2	POLR2A	chr2:97000252-97000536	HCT-116	colon:	n/a	n/a
3	ZNF384	chr2:97000317-97000498	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:97000297-97000662	HepG2	liver:	n/a	n/a
5	EBF1	chr2:97000315-97000524	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:97000390-97000732	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96929963..96932171-chr2:96999935..97002452,2	K562	blood:
2	chr2:96929992..96934856-chr2:96999935..97004454,8	K562	blood:
3	chr2:96968671..96973165-chr2:96996066..97004511,14	MCF-7	breast:
4	chr2:96994464..96999026-chr2:96999064..97001016,4	MCF-7	breast:
5	chr2:96954952..96956896-chr2:96999243..97002059,2	MCF-7	breast:
6	chr2:96969192..96974477-chr2:96999948..97003661,14	K562	blood:
7	chr2:96872884..96875870-chr2:96999913..97003204,4	MCF-7	breast:
8	chr2:96970144..96972526-chr2:96999842..97002907,4	MCF-7	breast:

No data

Variant related genes	Relation type
NCAPH	TF binding region
ENSG00000135956	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000144028	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1081717	0.95[EUR][1000 genomes]
rs2579502	0.85[MEX][hapmap]
rs2579505	0.84[CEU][hapmap]
rs582014	0.88[CEU][hapmap]
rs596069	0.96[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs631746	0.82[EUR][1000 genomes]
rs674920	0.81[EUR][1000 genomes]
rs772156	1.00[CEU][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs772159	0.96[CEU][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs772160	0.92[CEU][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs772161	0.82[EUR][1000 genomes]
rs772174	0.94[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs772177	0.84[CEU][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs772173	ITPRIPL1	cis	lung	GTEx
rs772173	LOC285033	cis	parietal	SCAN
rs772173	ZNF514	cis	parietal	SCAN
rs772173	ADRA2B	cis	cerebellum	SCAN
rs772173	ITPRIPL1	cis	Esophagus Mucosa	GTEx
rs772173	KIAA1310	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96991600-97000400	Weak transcription	Brain Substantia Nigra	brain
2	chr2:96991600-97000400	Weak transcription	Lung	lung
3	chr2:96991800-97000400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:96991800-97000400	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:96991800-97000400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:96991800-97000400	Weak transcription	Fetal Kidney	kidney
7	chr2:96991800-97000400	Weak transcription	Right Atrium	heart
8	chr2:96991800-97000800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:96991800-97000800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:96992200-97000400	Weak transcription	Primary B cells from cord blood	blood
11	chr2:96992200-97000400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:96992200-97000400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:96992200-97000400	Weak transcription	Pancreas	Pancrea
14	chr2:96992200-97000600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:96992400-97000400	Weak transcription	Primary T cells from cord blood	blood
16	chr2:96992400-97000600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:96992400-97000600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:96992600-97000400	Weak transcription	Esophagus	oesophagus
19	chr2:96992600-97000400	Weak transcription	Fetal Intestine Small	intestine
20	chr2:96992600-97000600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:96992600-97000600	Weak transcription	Right Ventricle	heart
22	chr2:96992600-97000800	Weak transcription	Spleen	Spleen
23	chr2:96992800-97000400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:96992800-97000400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:96992800-97000400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:96993400-97000400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:96993600-97000800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:96993800-97000600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:96994000-97000600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:96994000-97000600	Weak transcription	Fetal Brain Female	brain
31	chr2:96994000-97000800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:96994200-97000400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:96994200-97000600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:96994400-97000400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:96994400-97000400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:96994400-97000400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:96994600-97000400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:96994600-97000400	Weak transcription	Brain Germinal Matrix	brain
39	chr2:96994600-97000400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:96994600-97000400	Weak transcription	Fetal Thymus	thymus
41	chr2:96994600-97000600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:96994800-97000400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:96994800-97000400	Weak transcription	Fetal Stomach	stomach
44	chr2:96994800-97000600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:96995200-97000400	Weak transcription	NH-A	brain
46	chr2:96995400-97000400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:96995600-97000400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:96995800-97000400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:96995800-97000400	Weak transcription	Fetal Lung	lung
50	chr2:96995800-97000400	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links