Variant report

Variant	rs2101632
Chromosome Location	chr3:112321423-112321424
allele	C/T
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	NFATC1	chr3:112320973-112321470	GM12878	blood:	n/a	n/a
2	NFIC	chr3:112320944-112321500	GM12878	blood:	n/a	n/a
3	SPI1	chr3:112321053-112321471	GM12891	blood:	n/a	n/a
4	MEF2C	chr3:112320888-112321503	GM12878	blood:	n/a	chr3:112321185-112321200
5	MEF2A	chr3:112320891-112321529	GM12878	blood:	n/a	n/a
6	NFIC	chr3:112320923-112321508	GM12878	blood:	n/a	n/a
7	BATF	chr3:112321009-112321476	GM12878	blood:	n/a	n/a
8	SPI1	chr3:112321005-112321498	GM12878	blood:	n/a	n/a
9	ATF2	chr3:112320923-112321541	GM12878	blood:	n/a	n/a
10	IRF4	chr3:112320939-112321512	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC35A5-1	chr3:112315667-112322287	XLOC_002759

Variant related genes	Relation type
ENSG00000272761	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11489073	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11706550	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1512005	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1512006	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1844089	0.80[ASN][1000 genomes]
rs1877363	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1994713	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131008	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2172196	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279532	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280066	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2464611	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2633578	0.80[ASN][1000 genomes]
rs2633580	0.80[ASN][1000 genomes]
rs2633582	0.80[ASN][1000 genomes]
rs2633584	0.80[ASN][1000 genomes]
rs2638016	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638017	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638018	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638022	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638031	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638037	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638042	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638045	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2668217	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668220	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668222	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668223	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2705517	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705543	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705566	0.80[ASN][1000 genomes]
rs28866814	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2933142	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2952323	0.80[ASN][1000 genomes]
rs2952326	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2952327	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34233684	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732815	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682413	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5000995	0.85[EUR][1000 genomes]
rs6792947	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7625366	0.82[EUR][1000 genomes]
rs7652377	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs766968	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9288954	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9756562	0.80[ASN][1000 genomes]
rs9809247	0.82[EUR][1000 genomes]
rs9848054	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9866734	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9869455	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9869579	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS 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	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2101632	SLC35A5	cis	Thyroid	GTEx
rs2101632	SLC35A5	cis	Artery Tibial	GTEx
rs2101632	SLC35A5	cis	Nerve Tibial	GTEx
rs2101632	SLC35A5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
2	chr3:112281800-112325400	Weak transcription	Gastric	stomach
3	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
5	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:112298600-112325200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:112300200-112331000	Weak transcription	Lung	lung
11	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
12	chr3:112302600-112322800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:112302800-112324200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:112303600-112322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:112303800-112324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:112305000-112324200	Weak transcription	Fetal Brain Male	brain
17	chr3:112305200-112323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:112305200-112323600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:112305400-112323400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:112305400-112324000	Weak transcription	Brain Anterior Caudate	brain
21	chr3:112305400-112330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:112305600-112324200	Weak transcription	Fetal Kidney	kidney
23	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
24	chr3:112307400-112329000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:112311600-112330600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:112311600-112331000	Weak transcription	Psoas Muscle	Psoas
27	chr3:112312400-112324200	Weak transcription	Ovary	ovary
28	chr3:112312400-112325200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:112312400-112326800	Weak transcription	Fetal Lung	lung
30	chr3:112312400-112331000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:112312600-112322000	Weak transcription	HUVEC	blood vessel
32	chr3:112312600-112323000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:112312600-112323400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:112312600-112323600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:112312600-112323600	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:112312600-112324200	Weak transcription	Brain Angular Gyrus	brain
37	chr3:112312600-112330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
40	chr3:112316000-112327400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:112316200-112321800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:112316200-112323600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:112316400-112321600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:112316400-112323400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:112316400-112333600	Weak transcription	A549	lung
47	chr3:112316600-112321800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:112316600-112337600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:112316800-112323000	Weak transcription	NHDF-Ad	bronchial
50	chr3:112316800-112323600	Weak transcription	Primary T cells from cord blood	blood

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