Variant report

Variant	rs3762410
Chromosome Location	chr1:97189288-97189289
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:97185840..97188668-chr1:97188930..97190541,2	K562	blood:
2	chr1:97183615..97185204-chr1:97188330..97190541,2	K562	blood:

Variant related genes	Relation type
ENSG00000117569	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1032541	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165703	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165704	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165711	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165712	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1155474	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12071263	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12076288	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12079217	0.85[YRI][hapmap]
rs12080617	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12082632	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12086822	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12087010	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12087375	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091544	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12563538	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563540	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566237	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12568725	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12727525	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12734155	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12735550	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12735718	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12738081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749680	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1325754	0.83[EUR][1000 genomes]
rs1472341	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17115588	0.83[EUR][1000 genomes]
rs17115608	0.90[EUR][1000 genomes]
rs17115636	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17115644	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17115758	0.83[EUR][1000 genomes]
rs2101875	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2101876	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs273867	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs273871	0.86[EUR][1000 genomes]
rs273872	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs273873	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs273874	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs273878	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs273879	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs273880	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs273882	0.83[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs273883	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs273884	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28680499	0.83[EUR][1000 genomes]
rs34057734	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34367318	0.81[EUR][1000 genomes]
rs34534988	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34556757	0.83[EUR][1000 genomes]
rs34575842	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34658983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34940124	0.87[EUR][1000 genomes]
rs35304132	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35387107	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35540154	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35860087	0.83[EUR][1000 genomes]
rs3945004	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4950002	0.83[EUR][1000 genomes]
rs4950004	0.90[EUR][1000 genomes]
rs4950012	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531182	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs54790	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs661203	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66533250	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6667421	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6677128	0.83[EUR][1000 genomes]
rs6677843	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679882	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6680078	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6682629	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66945820	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6698118	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6701205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67075994	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68171384	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72721923	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72721957	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7513314	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7534302	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7541317	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs969953	0.82[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3762410	PTBP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97186400-97189600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:97186400-97189600	Active TSS	NHDF-Ad	bronchial
3	chr1:97186400-97190000	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr1:97186600-97189400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:97186600-97189600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:97186600-97189800	Active TSS	NHLF	lung
7	chr1:97186600-97190200	Active TSS	Stomach Smooth Muscle	stomach
8	chr1:97186800-97189400	Active TSS	Brain Cingulate Gyrus	brain
9	chr1:97186800-97189400	Active TSS	Brain Hippocampus Middle	brain
10	chr1:97186800-97189400	Active TSS	Fetal Stomach	stomach
11	chr1:97186800-97190000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:97187000-97189400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr1:97187000-97189600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:97187000-97189600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr1:97187000-97189800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:97187000-97189800	Active TSS	GM12878-XiMat	blood
17	chr1:97187200-97189400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:97187200-97189400	Active TSS	HMEC	breast
19	chr1:97187400-97191000	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr1:97188000-97189400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:97188000-97189400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:97188000-97189600	Active TSS	Brain Germinal Matrix	brain
23	chr1:97188000-97196200	Weak transcription	Spleen	Spleen
24	chr1:97188200-97189400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr1:97188200-97189400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr1:97188200-97189600	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr1:97188200-97189600	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr1:97188200-97189600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:97188200-97189600	Flanking Active TSS	HUVEC	blood vessel
30	chr1:97188200-97189800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:97188200-97189800	Transcr. at gene 5' and 3'	K562	blood
32	chr1:97188400-97189400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr1:97188400-97189400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr1:97188400-97189600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
35	chr1:97188400-97189600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:97188400-97189800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
37	chr1:97188400-97189800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
38	chr1:97188400-97189800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:97188400-97189800	Weak transcription	Pancreas	Pancrea
40	chr1:97188400-97189800	Weak transcription	Small Intestine	intestine
41	chr1:97188400-97191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:97188400-97193400	Weak transcription	Left Ventricle	heart
43	chr1:97188400-97198600	Weak transcription	Gastric	stomach
44	chr1:97188400-97202200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:97188400-97206800	Weak transcription	Lung	lung
46	chr1:97188600-97189400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:97188600-97189400	Flanking Active TSS	Fetal Lung	lung
48	chr1:97188600-97189400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr1:97188600-97189400	Flanking Active TSS	HepG2	liver
50	chr1:97188600-97189800	Enhancers	Primary neutrophils fromperipheralblood	blood

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