Variant report

Variant	rs772175
Chromosome Location	chr2:96944553-96944554
allele	A/G
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	chr2:96942515-96945421	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:96944251-96945068	K562	blood:	n/a	n/a
3	POLR2A	chr2:96943098-96944662	GM12892	blood:	n/a	n/a
4	POLR2A	chr2:96944281-96944749	K562	blood:	n/a	n/a
5	POLR2A	chr2:96944490-96945400	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:96943010-96945598	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:96944403-96944685	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr2:96942938-96945253	A549	lung:	n/a	n/a
9	POLR2A	chr2:96944362-96944779	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96929774..96935946-chr2:96940519..96946631,7	K562	blood:
2	chr2:96939108..96946297-chr2:96949498..96959663,15	MCF-7	breast:
3	chr2:96942551..96945806-chr2:96946996..96949678,4	K562	blood:

Variant related genes	Relation type
SNRNP200	TF binding region
ENSG00000144028	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000144021	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10183151	0.95[CEU][hapmap]
rs11680950	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs1168965	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs1168966	0.86[CEU][hapmap]
rs1168968	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs1168970	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1168974	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs1168975	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs1168976	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs11693248	0.84[AMR][1000 genomes]
rs13019188	0.80[CEU][hapmap]
rs1657502	0.82[CEU][hapmap]
rs2229169	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs2301707	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2312955	0.90[CEU][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs2692893	0.84[ASW][hapmap];0.86[CEU][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs2692894	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs2969490	0.86[CEU][hapmap]
rs2969491	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs3821051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4426564	0.90[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs4907299	0.90[CEU][hapmap];0.82[TSI][hapmap]
rs58448550	0.81[AMR][1000 genomes]
rs648225	0.87[AMR][1000 genomes]
rs749457	0.82[CEU][hapmap]
rs749459	0.82[CEU][hapmap]
rs7604842	0.95[CEU][hapmap]
rs772154	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs772178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs810057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs893173	0.82[CEU][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv984450	chr2:96936273-96951139	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs772175	CIAO1	cis	lymphoblastoid	seeQTL
rs772175	ADRA2B	cis	Thyroid	GTEx
rs772175	FAHD2CP	cis	Muscle Skeletal	GTEx
rs772175	MGAT4A	cis	parietal	SCAN
rs772175	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs772175	ADRA2B	cis	Nerve Tibial	GTEx
rs772175	GPAT2	cis	Muscle Skeletal	GTEx
rs772175	GPAT2	cis	Stomach	GTEx
rs772175	FAHD2CP	cis	lung	GTEx
rs772175	MRPL30	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96932800-96970400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:96933200-96970200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:96933200-96970400	Weak transcription	Right Atrium	heart
4	chr2:96933400-96956800	Strong transcription	Placenta	Placenta
5	chr2:96933400-96957400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:96933400-96968800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:96933400-96969000	Strong transcription	Left Ventricle	heart
8	chr2:96933400-96969200	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr2:96933400-96969400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:96933400-96969400	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr2:96933400-96970200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:96933400-96970200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:96933400-96970200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:96933400-96970200	Strong transcription	Fetal Lung	lung
15	chr2:96933400-96970200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:96933600-96960200	Strong transcription	Liver	Liver
17	chr2:96933600-96965800	Strong transcription	Lung	lung
18	chr2:96933600-96966800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:96933600-96966800	Strong transcription	Brain Germinal Matrix	brain
20	chr2:96933600-96967200	Strong transcription	Brain Angular Gyrus	brain
21	chr2:96933600-96969400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:96933600-96969400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:96933600-96969400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr2:96933600-96969600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr2:96933600-96969600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr2:96933600-96969800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:96933600-96969800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:96933600-96969800	Strong transcription	Fetal Intestine Small	intestine
29	chr2:96933600-96969800	Strong transcription	Fetal Stomach	stomach
30	chr2:96933600-96969800	Strong transcription	Hela-S3	cervix
31	chr2:96933600-96970000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:96933600-96970000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:96933600-96970000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:96933600-96970200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr2:96933600-96970200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:96933600-96970200	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:96933600-96970200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr2:96933800-96946200	Strong transcription	NHLF	lung
39	chr2:96933800-96953200	Strong transcription	GM12878-XiMat	blood
40	chr2:96933800-96962200	Strong transcription	Adipose Nuclei	Adipose
41	chr2:96933800-96966800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:96933800-96967000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:96933800-96968000	Strong transcription	Fetal Thymus	thymus
44	chr2:96933800-96969200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:96933800-96969400	Strong transcription	Primary T cells from cord blood	blood
46	chr2:96933800-96969400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:96933800-96969400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:96933800-96969400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:96933800-96969800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:96933800-96969800	Strong transcription	Fetal Intestine Large	intestine

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