Variant report

Variant	rs12500173
Chromosome Location	chr4:103997683-103997684
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:291)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:291 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:103996999-103998180	GM12892	blood:	n/a	n/a
2	FOXP2	chr4:103997488-103997847	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr4:103997293-103998185	HCT-116	colon:	n/a	n/a
4	POLR2A	chr4:103997049-103998170	K562	blood:	n/a	n/a
5	POLR2A	chr4:103997088-103998235	GM12892	blood:	n/a	n/a
6	POLR2A	chr4:103997123-103998189	K562	blood:	n/a	n/a
7	ZBTB33	chr4:103997426-103998230	SK-N-SH	brain:	n/a	chr4:103997921-103997936
8	POLR2A	chr4:103996714-103998426	PBDE	blood:	n/a	n/a
9	MXI1	chr4:103996954-103998441	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:103997069-103998094	GM18526	blood:	n/a	n/a
11	MAX	chr4:103997385-103998133	HUVEC	blood vessel:	n/a	chr4:103997516-103997523
12	GTF2F1	chr4:103996994-103998369	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr4:103996893-103998379	GM12892	blood:	n/a	n/a
14	MYC	chr4:103997383-103997932	MCF-7	breast:	n/a	chr4:103997516-103997523
15	TAF1	chr4:103997667-103998083	GM12891	blood:	n/a	n/a
16	TAF1	chr4:103997286-103998078	H1-neurons	neurons:	n/a	n/a
17	TAF1	chr4:103997244-103998021	HepG2	liver:	n/a	n/a
18	HDAC2	chr4:103997356-103998049	HepG2	liver:	n/a	n/a
19	YY1	chr4:103997165-103998123	GM12892	blood:	n/a	n/a
20	CTCF	chr4:103997681-103997783	GM19240	blood:	n/a	n/a
21	POLR2A	chr4:103997331-103998027	MCF-7	breast:	n/a	n/a
22	YY1	chr4:103997545-103997847	GM12891	blood:	n/a	n/a
23	STAT5A	chr4:103996806-103998043	GM12878	blood:	n/a	n/a
24	TAF1	chr4:103997397-103998071	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:103997377-103998154	U87	brain:	n/a	n/a
26	MAZ	chr4:103997127-103998078	K562	blood:	n/a	chr4:103997516-103997523
27	CTCF	chr4:103997660-103997810	NHEK	skin:	n/a	n/a
28	CTCF	chr4:103997680-103997830	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:103997492-103998103	PANC-1	pancreas:	n/a	n/a
30	MYC	chr4:103996697-103998518	K562	blood:	n/a	chr4:103997516-103997523
31	POLR2A	chr4:103997107-103998139	K562	blood:	n/a	n/a
32	SMC3	chr4:103997057-103997925	Hela-S3	cervix:	n/a	n/a
33	TBP	chr4:103996493-103998480	HepG2	liver:	n/a	n/a
34	POLR2A	chr4:103997245-103998166	HUVEC	blood vessel:	n/a	n/a
35	TCF7L2	chr4:103997227-103998133	HCT-116	colon:	n/a	n/a
36	MYC	chr4:103997284-103998036	K562	blood:	n/a	chr4:103997516-103997523
37	EP300	chr4:103997313-103997984	HepG2	liver:	n/a	n/a
38	POLR2A	chr4:103997134-103998107	SK-N-MC	brain:	n/a	n/a
39	ZNF263	chr4:103996882-103998458	HEK293-T-REx	kidney:	n/a	n/a
40	POLR2A	chr4:103997224-103998067	MCF-7	breast:	n/a	n/a
41	REST	chr4:103997334-103997998	K562	blood:	n/a	n/a
42	TBP	chr4:103996996-103998404	K562	blood:	n/a	n/a
43	MAX	chr4:103997246-103997797	A549	lung:	n/a	chr4:103997516-103997523
44	CTBP2	chr4:103997165-103998101	H1-hESC	embryonic stem cell:	n/a	n/a
45	KAP1	chr4:103997484-103998306	U2OS	brain:	n/a	n/a
46	JUND	chr4:103997362-103998007	H1-hESC	embryonic stem cell:	n/a	n/a
47	GTF2B	chr4:103997630-103998097	K562	blood:	n/a	n/a
48	YY1	chr4:103997607-103997928	SK-N-SH_RA	brain:	n/a	n/a
49	SIN3A	chr4:103996934-103997819	GM12878	blood:	n/a	chr4:103997290-103997303 chr4:103997293-103997302
50	MAX	chr4:103996564-103998189	K562	blood:	n/a	chr4:103997516-103997523

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:103939785..103942134-chr4:103995950..103999337,3	MCF-7	breast:
2	chr4:103997335..103999148-chr4:104019345..104021953,2	K562	blood:
3	chr4:103939297..103941618-chr4:103997332..103999799,2	K562	blood:
4	chr19:49375381..49376148-chr4:103997436..103998111,2	Hela-S3	cervix:
5	chr4:103996463..103998722-chr4:104006148..104008232,2	K562	blood:
6	chr4:103986693..103989619-chr4:103992122..103998066,6	K562	blood:
7	chr4:103747144..103749225-chr4:103996606..103998315,2	K562	blood:
8	chr4:103789205..103791017-chr4:103995982..103997960,2	K562	blood:
9	chr4:103997337..103998985-chr4:104019484..104022200,2	K562	blood:
10	chr4:103747413..103749606-chr4:103996961..103999341,3	MCF-7	breast:
11	chr4:103997617..103999132-chr4:104006790..104008370,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BDH2-1	chr4:103997584-103998075	NONHSAT097623

No data

Variant related genes	Relation type
SLC9B2	TF binding region
ENSG00000164037	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000164038	Chromatin interaction
ENSG00000246560	Chromatin interaction
ENSG00000164039	Chromatin interaction
ENSG00000087074	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12508269	0.91[AMR][1000 genomes];0.81[EUR][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	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12500173	BDH2	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103995200-103998600	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr4:103995600-103998600	Active TSS	Fetal Brain Female	brain
3	chr4:103996000-103997800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr4:103996000-103998200	Active TSS	Brain Angular Gyrus	brain
5	chr4:103996000-103998600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:103996200-103998000	Active TSS	Liver	Liver
7	chr4:103996200-103998400	Active TSS	A549	lung
8	chr4:103996400-103998200	Active TSS	GM12878-XiMat	blood
9	chr4:103996400-103998400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:103996400-103998400	Active TSS	Brain Germinal Matrix	brain
11	chr4:103996400-103998600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:103996600-103998000	Active TSS	Fetal Lung	lung
13	chr4:103996600-103998200	Active TSS	Gastric	stomach
14	chr4:103996600-103998200	Active TSS	Lung	lung
15	chr4:103996600-103998400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:103996600-103998400	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr4:103996600-103998400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr4:103996600-103998400	Active TSS	Psoas Muscle	Psoas
19	chr4:103996600-103998400	Active TSS	Right Ventricle	heart
20	chr4:103996600-103998800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr4:103996800-103997800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:103996800-103998000	Active TSS	Fetal Thymus	thymus
23	chr4:103996800-103998000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr4:103996800-103998000	Active TSS	NHDF-Ad	bronchial
25	chr4:103996800-103998200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr4:103996800-103998200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:103996800-103998200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:103996800-103998200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:103996800-103998200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr4:103996800-103998200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:103996800-103998200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:103996800-103998200	Active TSS	Brain Hippocampus Middle	brain
33	chr4:103996800-103998200	Active TSS	Colon Smooth Muscle	Colon
34	chr4:103996800-103998200	Active TSS	Fetal Kidney	kidney
35	chr4:103996800-103998200	Active TSS	Ovary	ovary
36	chr4:103996800-103998200	Active TSS	HSMM	muscle
37	chr4:103996800-103998400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr4:103996800-103998400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:103996800-103998400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:103996800-103998400	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr4:103996800-103998400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:103996800-103998400	Active TSS	Fetal Muscle Trunk	muscle
43	chr4:103996800-103998600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr4:103996800-103998600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr4:103996800-103998600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:103996800-103998600	Active TSS	Fetal Brain Male	brain
47	chr4:103996800-103998600	Active TSS	Right Atrium	heart
48	chr4:103997000-103997800	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr4:103997000-103998000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr4:103997000-103998000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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