Variant report

Variant	rs7375038
Chromosome Location	chr3:121347927-121347928
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12489511	0.92[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs12631824	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13067629	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1492177	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1574655	0.90[EUR][1000 genomes]
rs1574735	0.90[EUR][1000 genomes]
rs1873645	1.00[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]
rs1919552	0.81[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs1919557	0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1986874	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2001390	0.90[EUR][1000 genomes]
rs2001391	0.94[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs2070179	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2840143	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35295338	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772127	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4478028	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4676684	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4676685	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4676686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438645	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438660	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs6770719	0.90[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs6791896	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792659	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794341	0.90[EUR][1000 genomes]
rs6794677	0.87[EUR][1000 genomes]
rs6802033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6803839	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6807711	0.94[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7429247	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7430165	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7611913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620842	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7646585	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes]
rs9289172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9681209	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs9809114	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9812411	0.94[ASW][hapmap];0.90[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes]
rs9829053	0.88[EUR][1000 genomes]
rs9832267	0.92[EUR][1000 genomes]
rs9835182	0.90[EUR][1000 genomes]
rs9854052	0.92[EUR][1000 genomes]
rs9861992	0.92[EUR][1000 genomes]
rs9864907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9876021	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers 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	18 gene(s)	inside rSNPs	diseases
6	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
7	nsv999349	chr3:121253990-121360206	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7375038	HCLS1	cis	multi-tissue	Pritchard
rs7375038	ADPRH	cis	parietal	SCAN
rs7375038	HCLS1	cis	lymphoblastoid	seeQTL
rs7375038	SLC15A2	cis	cerebellum	SCAN
rs7375038	MUC13	cis	cerebellum	SCAN
rs7375038	HCLS1	cis	Lymphoblastoid	GTEx
rs7375038	SLC15A2	cis	parietal	SCAN
rs7375038	CCDC58	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121341800-121348400	Weak transcription	Spleen	Spleen
2	chr3:121342000-121350000	Weak transcription	Liver	Liver
3	chr3:121343200-121348400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:121343400-121348000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr3:121343600-121348400	Weak transcription	Psoas Muscle	Psoas
6	chr3:121343800-121353000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:121345000-121349400	Strong transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:121345600-121348000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr3:121345600-121349600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:121345600-121376800	Weak transcription	Esophagus	oesophagus
11	chr3:121345800-121348600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:121345800-121350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:121346000-121348800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:121346200-121350000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:121346200-121351600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:121346400-121349000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:121346400-121349800	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:121346400-121351800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:121346400-121353200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:121346600-121348200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:121346600-121348400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:121346800-121348400	Weak transcription	GM12878-XiMat	blood
23	chr3:121346800-121351800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:121347000-121349200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:121347000-121349200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:121347000-121378000	Weak transcription	Right Ventricle	heart
27	chr3:121347200-121348800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:121347200-121349400	Enhancers	Fetal Heart	heart
29	chr3:121347200-121352600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:121347200-121364400	Strong transcription	Primary B cells from cord blood	blood
31	chr3:121347400-121348400	Weak transcription	Left Ventricle	heart
32	chr3:121347400-121349000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:121347400-121349000	Weak transcription	Dnd41	blood
34	chr3:121347400-121349600	Weak transcription	Thymus	Thymus
35	chr3:121347400-121349800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:121347400-121350800	Weak transcription	Right Atrium	heart
37	chr3:121347400-121352200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:121347400-121367200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:121347600-121350200	Weak transcription	HUVEC	blood vessel
40	chr3:121347600-121353000	Strong transcription	Fetal Thymus	thymus
41	chr3:121347600-121359400	Strong transcription	Primary T cells from cord blood	blood
42	chr3:121347600-121364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:121347600-121364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:121347600-121364600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:121347800-121349400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:121347800-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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