Variant report

Variant	rs2076041
Chromosome Location	chr22:32803952-32803953
allele	A/G
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	WRNIP1	chr22:32803829-32804049	GM12878	blood:	n/a	n/a
2	SPI1	chr22:32803017-32804038	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:32803479..32806391-chr22:32807402..32809274,3	MCF-7	breast:
2	chr22:32793471..32796323-chr22:32803063..32805279,2	MCF-7	breast:
3	chr22:32802183..32805062-chr22:32805761..32809013,3	MCF-7	breast:

Variant related genes	Relation type
RTCB	TF binding region
ENSG00000100220	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs11089557	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11089560	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11089564	0.81[ASN][1000 genomes]
rs11635	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11912349	0.88[ASN][1000 genomes]
rs12160141	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12160986	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12628702	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs136471	0.97[AMR][1000 genomes]
rs16987625	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16990258	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16990262	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16990269	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16990428	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16990430	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1810450	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2014356	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072816	0.99[ASN][1000 genomes]
rs2076045	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2281034	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2281035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294311	0.99[ASN][1000 genomes]
rs2294312	0.84[ASN][1000 genomes]
rs2294313	1.00[ASN][1000 genomes]
rs2294314	0.97[ASN][1000 genomes]
rs2413110	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2413111	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28404482	0.91[AMR][1000 genomes]
rs2899184	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35207231	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs45593940	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4577392	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5749408	0.84[EUR][1000 genomes]
rs5749409	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749410	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749411	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749413	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5749414	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5749416	0.92[ASN][1000 genomes]
rs5749421	0.82[ASN][1000 genomes]
rs5749426	0.80[ASN][1000 genomes]
rs5749427	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749428	0.99[ASN][1000 genomes]
rs5749429	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749433	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753988	0.88[AMR][1000 genomes]
rs5754000	0.94[AMR][1000 genomes]
rs5754001	0.97[AMR][1000 genomes]
rs5754003	0.97[AMR][1000 genomes]
rs5754005	0.97[AMR][1000 genomes]
rs5754006	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754007	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754008	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754009	0.94[AMR][1000 genomes]
rs5754010	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754011	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754012	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754017	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754018	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754019	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754021	0.94[AMR][1000 genomes]
rs5754023	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754025	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754029	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754031	0.82[AMR][1000 genomes]
rs5754032	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754033	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754035	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754039	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754042	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754045	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754046	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754047	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754048	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754050	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754063	0.82[ASN][1000 genomes]
rs5754065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754066	0.82[ASN][1000 genomes]
rs57606003	0.82[AMR][1000 genomes]
rs58028985	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58500302	0.94[AMR][1000 genomes]
rs58637580	0.82[AMR][1000 genomes]
rs59895149	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5998434	0.91[AMR][1000 genomes]
rs5998453	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5998457	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5998459	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5998471	0.83[ASN][1000 genomes]
rs5998475	1.00[ASN][1000 genomes]
rs713790	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72137940	0.84[ASN][1000 genomes]
rs72617300	0.89[AMR][1000 genomes]
rs72617301	0.91[AMR][1000 genomes]
rs72617302	0.97[AMR][1000 genomes]
rs72620403	0.91[AMR][1000 genomes]
rs72620404	0.97[AMR][1000 genomes]
rs72620405	0.97[AMR][1000 genomes]
rs72620406	0.97[AMR][1000 genomes]
rs72620407	0.97[AMR][1000 genomes]
rs72620408	0.97[AMR][1000 genomes]
rs7292163	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs737779	0.83[ASN][1000 genomes]
rs742096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2076041	SLC5A4	cis	Esophagus Muscularis	GTEx
rs2076041	SLC5A4	cis	Adipose Subcutaneous	GTEx
rs2076041	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL
rs2076041	SLC5A4	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32780800-32806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:32780800-32806400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:32781200-32804000	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr22:32781200-32804200	Strong transcription	Stomach Smooth Muscle	stomach
5	chr22:32781200-32804600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr22:32781200-32804600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr22:32781200-32804800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr22:32781200-32805000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr22:32781200-32805400	Strong transcription	Fetal Muscle Leg	muscle
10	chr22:32781200-32806600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr22:32781400-32804400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr22:32781400-32804600	Strong transcription	Fetal Thymus	thymus
13	chr22:32781400-32804600	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr22:32781400-32804600	Strong transcription	Dnd41	blood
15	chr22:32781400-32804800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr22:32781400-32804800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr22:32781400-32804800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr22:32781400-32804800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr22:32781400-32805000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr22:32781400-32805000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr22:32781400-32805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:32781400-32805000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr22:32781400-32805000	Strong transcription	Fetal Intestine Large	intestine
24	chr22:32781400-32805000	Strong transcription	Fetal Lung	lung
25	chr22:32781400-32805000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr22:32781400-32805000	Strong transcription	Left Ventricle	heart
27	chr22:32781400-32805000	Strong transcription	Osteobl	bone
28	chr22:32781400-32805200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr22:32781400-32805200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr22:32781400-32805600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr22:32781400-32806400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr22:32781400-32806600	Strong transcription	Placenta	Placenta
33	chr22:32781600-32804800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr22:32781600-32804800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr22:32781600-32805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr22:32781600-32805000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr22:32781600-32805400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr22:32781600-32806000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr22:32781800-32805000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr22:32782000-32804800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr22:32782200-32805200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr22:32782400-32804800	Strong transcription	Brain Hippocampus Middle	brain
43	chr22:32782800-32807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr22:32783000-32805000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr22:32783200-32806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr22:32783400-32805000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr22:32785600-32804400	Strong transcription	Colon Smooth Muscle	Colon
48	chr22:32785600-32804800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr22:32788000-32805000	Strong transcription	Primary T cells from cord blood	blood
50	chr22:32788200-32804600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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