Variant report

Variant	rs71520819
Chromosome Location	chr8:104511978-104511979
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	SIN3A	chr8:104510669-104514416	H1-hESC	embryonic stem cell:	n/a	chr8:104512440-104512453 chr8:104512690-104512703 chr8:104512322-104512335 chr8:104514131-104514145 chr8:104511737-104511746 chr8:104511075-104511086 chr8:104514132-104514141
2	CTCF	chr8:104511907-104511986	GM19239	blood:	n/a	n/a
3	JUND	chr8:104511935-104512109	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr8:104510510-104512074	HCT-116	colon:	n/a	chr8:104511715-104511725 chr8:104511045-104511055
5	EBF1	chr8:104511946-104512191	GM12878	blood:	n/a	n/a
6	POLR2A	chr8:104510628-104512178	HCT-116	colon:	n/a	n/a
7	MAX	chr8:104511103-104512351	H1-hESC	embryonic stem cell:	n/a	chr8:104511715-104511725
8	CTCF	chr8:104511566-104511980	GM12891	blood:	n/a	n/a
9	POLR2A	chr8:104511885-104512167	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr8:104511860-104512010	SK-N-SH_RA	brain:	n/a	n/a
11	ZNF263	chr8:104510341-104512321	HEK293-T-REx	kidney:	n/a	chr8:104510771-104510780 chr8:104511611-104511620
12	CTBP2	chr8:104510977-104513239	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3AK20	chr8:104511853-104512211	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF1	chr8:104511328-104512173	H1-neurons	neurons:	n/a	n/a
15	TCF12	chr8:104510704-104512276	ECC-1	luminal epithelium:	n/a	chr8:104511704-104511711
16	MAX	chr8:104510619-104511995	MCF-7	breast:	n/a	chr8:104511715-104511725 chr8:104511045-104511055
17	BACH1	chr8:104511924-104512119	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr8:104511151-104512401	H1-neurons	neurons:	n/a	n/a
19	CTCF	chr8:104511621-104511983	MCF-7	breast:	n/a	n/a
20	REST	chr8:104511958-104512244	SK-N-SH	brain:	n/a	n/a
21	ZBTB7A	chr8:104511086-104512177	ECC-1	luminal epithelium:	n/a	chr8:104511711-104511720
22	POLR2A	chr8:104510780-104513316	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr8:104511858-104512133	HCT-116	colon:	n/a	n/a
24	REST	chr8:104511893-104512303	ECC-1	luminal epithelium:	n/a	chr8:104512276-104512296
25	ZBTB7A	chr8:104510843-104513086	ECC-1	luminal epithelium:	n/a	chr8:104511711-104511720
26	EGR1	chr8:104511863-104512267	H1-hESC	embryonic stem cell:	n/a	chr8:104512088-104512098 chr8:104512088-104512101 chr8:104512083-104512105 chr8:104512089-104512098 chr8:104512088-104512101 chr8:104512088-104512101 chr8:104512088-104512101 chr8:104512089-104512099
27	MXI1	chr8:104510187-104514952	SK-N-SH	brain:	n/a	n/a
28	TBP	chr8:104511944-104512114	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF7L2	chr8:104510767-104512119	HCT-116	colon:	n/a	n/a
30	HDAC2	chr8:104511844-104512132	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104424987..104428689-chr8:104510615..104514344,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC25A32-3	chr8:104510404-104512975	NONHSAT128193

Variant related genes	Relation type
ENSG00000253477	TF binding region
RIMS2	TF binding region
ENSG00000164933	Chromatin interaction
ENSG00000164934	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10097034	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10097208	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10099086	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10106671	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10955317	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10955318	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11776639	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11783518	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11784011	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12114365	0.85[ASN][1000 genomes]
rs12544166	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12544298	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12547300	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12550530	0.82[ASN][1000 genomes]
rs12550536	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12678622	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12680638	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12682484	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13248060	0.85[ASN][1000 genomes]
rs13264879	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17805787	0.83[ASN][1000 genomes]
rs2080609	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2080610	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2118059	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28802649	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34458961	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35101283	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35442232	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35667758	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35745796	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36056848	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36093974	0.85[ASN][1000 genomes]
rs4517090	0.81[EUR][1000 genomes]
rs4641028	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4734711	0.85[ASN][1000 genomes]
rs4734712	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4734714	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4734716	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4734717	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4734719	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61247429	0.85[ASN][1000 genomes]
rs6468875	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68184585	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6988627	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6993717	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6999864	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72675499	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72677619	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7813485	0.82[ASN][1000 genomes]
rs7817860	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7842405	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7843512	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv1020476	chr8:104312212-104924482	Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539704	chr8:104312212-104924482	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1023048	chr8:104355188-104872701	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv539705	chr8:104355188-104872701	ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1021345	chr8:104361854-104879684	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1032085	chr8:104362187-104878345	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv1034183	chr8:104369940-104814008	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv539707	chr8:104369940-104814008	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	esv2753239	chr8:104404824-104545824	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv3384862	chr8:104511126-104513424	Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs71520819	RIMS2	cis	Thyroid	GTEx
rs71520819	RP11-1C8.4	cis	Thyroid	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104510400-104514200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:104510400-104514400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr8:104510400-104514600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr8:104510400-104514800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr8:104510400-104515000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr8:104510600-104512600	Active TSS	Brain Cingulate Gyrus	brain
7	chr8:104510600-104513200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr8:104510600-104514200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:104510600-104514200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr8:104510600-104514200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr8:104510600-104514200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr8:104510600-104514400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr8:104510600-104514400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr8:104510600-104514600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr8:104510600-104514600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr8:104510600-104514800	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr8:104510800-104512000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr8:104510800-104512000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
19	chr8:104510800-104512400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr8:104510800-104512800	Active TSS	Brain Substantia Nigra	brain
21	chr8:104510800-104512800	Bivalent Enhancer	Fetal Thymus	thymus
22	chr8:104510800-104513000	Bivalent/Poised TSS	A549	lung
23	chr8:104510800-104513600	Bivalent/Poised TSS	HSMM	muscle
24	chr8:104510800-104513800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr8:104510800-104513800	Bivalent Enhancer	Spleen	Spleen
26	chr8:104510800-104514000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr8:104510800-104514200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr8:104510800-104514200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr8:104510800-104514200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr8:104510800-104514400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr8:104510800-104515000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:104511000-104512000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
33	chr8:104511000-104512200	Bivalent/Poised TSS	HSMMtube	muscle
34	chr8:104511000-104512400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr8:104511000-104512400	Active TSS	NHEK	skin
36	chr8:104511000-104512800	Bivalent/Poised TSS	NHLF	lung
37	chr8:104511000-104513000	Active TSS	Brain Anterior Caudate	brain
38	chr8:104511000-104513200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr8:104511000-104513600	Active TSS	HepG2	liver
40	chr8:104511000-104515200	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr8:104511200-104512400	Active TSS	Brain Germinal Matrix	brain
42	chr8:104511200-104513000	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr8:104511400-104512000	Enhancers	Fetal Heart	heart
44	chr8:104511400-104512400	Enhancers	Primary B cells from cord blood	blood
45	chr8:104511400-104512400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr8:104511400-104512800	Active TSS	NH-A	brain
47	chr8:104511400-104513000	Enhancers	Liver	Liver
48	chr8:104511400-104513600	Bivalent Enhancer	Placenta	Placenta
49	chr8:104511400-104514200	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr8:104511400-104514400	Active TSS	NHDF-Ad	bronchial

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