Variant report

Variant	rs7552545
Chromosome Location	chr1:97188394-97188395
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:97187688..97188569-chr12:6643781..6644363,2	Hela-S3	cervix:
2	chr1:97183615..97185204-chr1:97188330..97190541,2	K562	blood:

Variant related genes	Relation type
ENSG00000111640	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10875032	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165710	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165714	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12022396	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12069825	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12071257	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[EUR][1000 genomes]
rs12075038	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12097991	0.88[EUR][1000 genomes]
rs1591868	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17524886	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2021640	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2066112	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2088251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2172980	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs273860	0.84[EUR][1000 genomes]
rs273863	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs273865	0.82[EUR][1000 genomes]
rs273870	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs273875	0.84[EUR][1000 genomes]
rs273876	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs273877	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs273885	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs273886	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3009394	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35137759	0.82[EUR][1000 genomes]
rs3748784	0.92[EUR][1000 genomes]
rs3748785	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3762409	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762411	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3908925	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4576698	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4949941	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4950005	0.94[EUR][1000 genomes]
rs541461	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56257350	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603231	0.81[ASN][1000 genomes]
rs6661004	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6673531	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6683362	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6698585	0.93[EUR][1000 genomes]
rs7531045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533165	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7548031	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7554256	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7554259	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs996315	0.97[EUR][1000 genomes];0.88[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	nsv830681	chr1:97165786-97338064	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv3414899	chr1:97187980-97211076	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
3	esv1797391	chr1:97188394-97293023	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1801594	chr1:97188394-97293023	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7552545	PTBP2	Cis_1M	lymphoblastoid	RTeQTL
rs7552545	PTBP2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97186400-97188600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:97186400-97188600	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr1:97186400-97189600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:97186400-97189600	Active TSS	NHDF-Ad	bronchial
5	chr1:97186400-97190000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:97186600-97188400	Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr1:97186600-97188400	Active TSS	Pancreas	Pancrea
8	chr1:97186600-97188600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr1:97186600-97188600	Active TSS	Placenta	Placenta
10	chr1:97186600-97188800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:97186600-97188800	Active TSS	Rectal Smooth Muscle	rectum
12	chr1:97186600-97189000	Active TSS	Fetal Intestine Large	intestine
13	chr1:97186600-97189000	Active TSS	Fetal Thymus	thymus
14	chr1:97186600-97189000	Active TSS	Psoas Muscle	Psoas
15	chr1:97186600-97189200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:97186600-97189200	Active TSS	Colonic Mucosa	Colon
17	chr1:97186600-97189200	Active TSS	Colon Smooth Muscle	Colon
18	chr1:97186600-97189200	Active TSS	Fetal Brain Male	brain
19	chr1:97186600-97189200	Active TSS	Fetal Muscle Trunk	muscle
20	chr1:97186600-97189200	Active TSS	Fetal Muscle Leg	muscle
21	chr1:97186600-97189200	Active TSS	Ovary	ovary
22	chr1:97186600-97189200	Active TSS	Thymus	Thymus
23	chr1:97186600-97189400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:97186600-97189600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr1:97186600-97189800	Active TSS	NHLF	lung
26	chr1:97186600-97190200	Active TSS	Stomach Smooth Muscle	stomach
27	chr1:97186800-97188400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:97186800-97188400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:97186800-97188400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:97186800-97188400	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr1:97186800-97188400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:97186800-97188400	Active TSS	Gastric	stomach
33	chr1:97186800-97188400	Active TSS	Left Ventricle	heart
34	chr1:97186800-97188400	Active TSS	Lung	lung
35	chr1:97186800-97188600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:97186800-97188600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:97186800-97188600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:97186800-97188600	Active TSS	Esophagus	oesophagus
39	chr1:97186800-97188600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr1:97186800-97188600	Active TSS	HepG2	liver
41	chr1:97186800-97188800	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:97186800-97188800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr1:97186800-97188800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr1:97186800-97188800	Active TSS	Brain Substantia Nigra	brain
45	chr1:97186800-97188800	Active TSS	Fetal Kidney	kidney
46	chr1:97186800-97188800	Active TSS	A549	lung
47	chr1:97186800-97189000	Active TSS	Right Ventricle	heart
48	chr1:97186800-97189000	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr1:97186800-97189000	Active TSS	HSMM	muscle
50	chr1:97186800-97189200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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