Variant report

Variant	rs7732198
Chromosome Location	chr5:112379659-112379660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112378846..112379838-chr5:112666004..112666840,2	MCF-7	breast:
2	chr5:112377774..112380762-chr5:112388761..112390824,2	K562	blood:
3	chr5:112378867..112380762-chr5:112388761..112390439,2	K562	blood:
4	chr5:112363970..112366861-chr5:112379639..112381179,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10039618	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10045658	0.84[CHB][hapmap]
rs10054158	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10058407	0.81[CHB][hapmap]
rs10223151	0.84[CHB][hapmap]
rs10223152	0.89[CHB][hapmap]
rs1057474	0.81[JPT][hapmap]
rs11241190	0.84[CHB][hapmap]
rs11744218	0.84[CHB][hapmap]
rs11744828	0.83[CHB][hapmap]
rs11744956	0.84[CHB][hapmap]
rs11749921	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11750093	0.84[CHB][hapmap]
rs1363333	0.84[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs1549181	0.81[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs2227948	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3857434	0.81[JPT][hapmap]
rs3890775	0.84[CHB][hapmap]
rs4073358	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4073359	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4074190	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4075350	0.84[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs4283779	0.84[CHB][hapmap]
rs4301226	0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs4397121	0.84[CHB][hapmap]
rs4428399	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4599529	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4645326	0.84[CHB][hapmap]
rs4705539	0.84[CHB][hapmap]
rs4705750	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs4705752	0.81[JPT][hapmap]
rs4705755	0.88[EUR][1000 genomes]
rs4705756	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4705758	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4705762	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs6594665	0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs6594680	0.84[CHB][hapmap]
rs6861166	0.84[CHB][hapmap]
rs6862481	0.89[CHB][hapmap]
rs6866566	0.84[CHB][hapmap]
rs6873623	0.84[CHB][hapmap]
rs6877570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6877769	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6879138	0.84[CHB][hapmap]
rs6879589	0.84[CHB][hapmap];0.89[ASN][1000 genomes]
rs6879633	0.90[CHB][hapmap]
rs6879942	0.84[CHB][hapmap]
rs6893016	0.84[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs6893389	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6894219	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs6894937	0.82[EUR][1000 genomes]
rs6898297	0.84[CHB][hapmap]
rs7670	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs7701781	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs7708603	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7713290	0.83[CHB][hapmap]
rs7713336	0.84[CHB][hapmap]
rs7714010	0.84[CHB][hapmap]
rs7714160	0.84[CHB][hapmap]
rs7714492	0.84[CHB][hapmap]
rs7714725	0.84[CHB][hapmap]
rs7731890	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7734411	0.84[CHB][hapmap]
rs7736823	0.84[CHB][hapmap]
rs9122	0.81[JPT][hapmap]
rs9326874	0.84[CHB][hapmap]
rs9326875	0.84[CHB][hapmap]
rs9784647	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv15902	chr5:112369563-112410775	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1817377	chr5:112373682-112389837	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv516887	chr5:112379659-112396174	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7732198	TSLP	cis	parietal	SCAN
rs7732198	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs7732198	DCP2	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112362800-112385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:112363600-112382800	Weak transcription	Fetal Intestine Small	intestine
3	chr5:112363800-112384600	Weak transcription	Aorta	Aorta
4	chr5:112363800-112386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
7	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:112364000-112389400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:112364200-112386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:112364800-112382800	Weak transcription	Fetal Intestine Large	intestine
11	chr5:112364800-112382800	Weak transcription	Fetal Thymus	thymus
12	chr5:112365800-112382200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:112368800-112382800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:112369200-112380200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:112369400-112382800	Strong transcription	Liver	Liver
16	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:112370600-112382800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:112370600-112396600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:112371000-112383400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:112371400-112382600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:112371400-112391400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:112371600-112394200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:112372600-112384000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:112372800-112396800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:112373000-112381400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:112373000-112382600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:112373000-112382800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:112373000-112383000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:112373000-112398800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:112373200-112399000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:112374600-112383200	Weak transcription	Fetal Kidney	kidney
33	chr5:112374800-112382400	Weak transcription	HSMMtube	muscle
34	chr5:112374800-112383200	Weak transcription	Osteobl	bone
35	chr5:112374800-112386000	Weak transcription	NHDF-Ad	bronchial
36	chr5:112374800-112386200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:112375000-112402600	Weak transcription	Pancreas	Pancrea
38	chr5:112375200-112384400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:112375400-112380000	Weak transcription	Lung	lung
40	chr5:112375400-112380600	Weak transcription	HMEC	breast
41	chr5:112377400-112379800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:112377400-112386400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr5:112377400-112389000	Weak transcription	Primary T cells from cord blood	blood
44	chr5:112378200-112379800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:112378200-112383000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:112378600-112379800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr5:112378600-112379800	Strong transcription	Esophagus	oesophagus
48	chr5:112378600-112379800	Enhancers	Ovary	ovary
49	chr5:112378600-112379800	Enhancers	NH-A	brain
50	chr5:112378800-112379800	Enhancers	Brain Anterior Caudate	brain

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