Variant report

Variant	rs5858
Chromosome Location	chr11:65120391-65120392
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:65120380-65120530	AG09319	gingival:	n/a	n/a
2	CTCF	chr11:65120340-65120490	BE2_C	brain:	n/a	n/a
3	CTCF	chr11:65120347-65120599	HUVEC	blood vessel:	n/a	n/a
4	CTCF	chr11:65120380-65120530	RPTEC	kidney:	n/a	n/a
5	CTCF	chr11:65120349-65120569	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr11:65120380-65120530	NB4	blood:	n/a	n/a
7	CTCF	chr11:65120344-65120616	K562	blood:	n/a	n/a
8	CTCF	chr11:65120380-65120530	NHLF	lung:	n/a	n/a
9	CTCF	chr11:65120320-65120470	HFF	foreskin:	n/a	n/a
10	CTCF	chr11:65120360-65120510	GM12873	blood:	n/a	n/a
11	CTCF	chr11:65120380-65120530	GM12878	blood:	n/a	n/a
12	CTCF	chr11:65120360-65120510	SAEC	small airway:	n/a	n/a
13	CTCF	chr11:65120343-65120539	GM12878	blood:	n/a	n/a
14	CTCF	chr11:65120300-65120450	HAc	cerebellar:	n/a	n/a
15	CTCF	chr11:65120360-65120510	AG10803	skin:	n/a	n/a
16	CTCF	chr11:65120360-65120510	GM06990	blood:	n/a	n/a
17	RAD21	chr11:65120336-65120552	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr11:65120280-65120430	HEK293	kidney:	n/a	n/a
19	CTCF	chr11:65120323-65120588	GM12878	blood:	n/a	n/a
20	CTCF	chr11:65120385-65120535	HepG2	liver:	n/a	n/a
21	CTCF	chr11:65120340-65120490	GM06990	blood:	n/a	n/a
22	CTCF	chr11:65120360-65120510	HBMEC	blood vessel:	n/a	n/a
23	POLR2A	chr11:65119954-65120492	SK-N-MC	brain:	n/a	n/a
24	CTCF	chr11:65120380-65120530	HMEC	breast:	n/a	n/a
25	YY1	chr11:65120309-65120599	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr11:65120380-65120530	BJ	skin:	n/a	n/a
27	CTCF	chr11:65120380-65120530	AG04449	skin:	n/a	n/a
28	CTCF	chr11:65120360-65120510	HepG2	liver:	n/a	n/a
29	CTCF	chr11:65120360-65120510	HUVEC	blood vessel:	n/a	n/a
30	CTCF	chr11:65120340-65120490	SK-N-SH_RA	brain:	n/a	n/a
31	CTCF	chr11:65120320-65120470	NHEK	skin:	n/a	n/a
32	CTCF	chr11:65120380-65120530	HRPEpiC	eye:	n/a	n/a
33	CTCF	chr11:65120012-65120779	A549	lung:	n/a	n/a
34	RAD21	chr11:65120323-65120566	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr11:65120320-65120619	IMR90	lung:	n/a	n/a
36	CTCF	chr11:65120360-65120510	AG09309	skin:	n/a	n/a
37	CTCF	chr11:65120380-65120530	HPF	lung:	n/a	n/a
38	CTCF	chr11:65120360-65120510	AoAF	blood vessel:	n/a	n/a
39	CTCF	chr11:65120300-65120450	HCM	heart:	n/a	n/a
40	CTCF	chr11:65120360-65120510	GM12864	blood:	n/a	n/a
41	CTCF	chr11:65120320-65120470	GM12873	blood:	n/a	n/a
42	CTCF	chr11:65120280-65120430	HFF-Myc	foreskin:	n/a	n/a
43	CTCF	chr11:65120380-65120530	K562	blood:	n/a	n/a
44	CTCF	chr11:65120360-65120510	HEEpiC	esophagus:	n/a	n/a
45	CTCF	chr11:65120360-65120510	A549	lung:	n/a	n/a
46	POLR2A	chr11:65119429-65120445	GM12878	blood:	n/a	n/a
47	CTCF	chr11:65120390-65120542	Medullo	brain:	n/a	n/a
48	CTCF	chr11:65120374-65120551	SK-N-SH_RA	brain:	n/a	n/a
49	CTCF	chr11:65120354-65120564	LNCaP	prostate:	n/a	n/a
50	CTCF	chr11:65120360-65120510	AG04450	lung:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65116418..65118589-chr11:65119582..65121612,3	K562	blood:
2	chr11:65083433..65086025-chr11:65118367..65121130,2	MCF-7	breast:
3	chr11:65119888..65122132-chr11:65123050..65125503,3	K562	blood:
4	chr11:65105171..65109589-chr11:65119360..65123181,4	K562	blood:
5	chr11:65045328..65049022-chr11:65119140..65122878,4	MCF-7	breast:
6	chr11:65084600..65086404-chr11:65120200..65124254,3	MCF-7	breast:
7	chr11:65116402..65157784-chr11:65261420..65278410,154	K562	blood:
8	chr11:65102149..65103973-chr11:65118677..65120435,2	MCF-7	breast:
9	chr11:65106450..65111070-chr11:65119360..65123401,6	K562	blood:
10	chr11:65111096..65115711-chr11:65116399..65121621,9	K562	blood:
11	chr11:65083110..65084794-chr11:65119604..65121339,2	K562	blood:
12	chr11:65112410..65115182-chr11:65119454..65121436,2	K562	blood:

No data

Variant related genes	Relation type
TIGD3	TF binding region
ENSG00000014138	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000149798	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000133884	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2904978	0.80[ASW][hapmap]
rs4930290	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs629710	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS 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	48 gene(s)	inside rSNPs	diseases
3	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
4	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
5	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
6	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5858	TIGD3	cis	Thyroid	GTEx
rs5858	DPF2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65103200-65121200	Strong transcription	Fetal Intestine Small	intestine
2	chr11:65103400-65120800	Strong transcription	Fetal Muscle Leg	muscle
3	chr11:65103400-65121200	Strong transcription	Fetal Stomach	stomach
4	chr11:65104400-65121400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:65105000-65121000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:65105600-65120400	Strong transcription	Primary T cells from cord blood	blood
7	chr11:65105600-65120400	Strong transcription	Fetal Lung	lung
8	chr11:65105600-65120600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:65105600-65120600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr11:65105600-65120800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:65105600-65121000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr11:65105600-65121000	Strong transcription	Osteobl	bone
13	chr11:65105600-65121200	Strong transcription	Fetal Intestine Large	intestine
14	chr11:65105600-65121400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:65105800-65120400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:65105800-65120400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:65105800-65120400	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr11:65105800-65120400	Strong transcription	Liver	Liver
19	chr11:65105800-65120400	Strong transcription	Fetal Brain Female	brain
20	chr11:65105800-65120400	Strong transcription	Hela-S3	cervix
21	chr11:65105800-65121000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:65105800-65121000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:65105800-65121200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:65106000-65120400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr11:65106000-65120400	Strong transcription	Spleen	Spleen
26	chr11:65106000-65121000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:65106000-65121000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:65106200-65120400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:65106200-65120400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:65106200-65121000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:65106400-65120400	Strong transcription	Dnd41	blood
32	chr11:65106400-65120800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr11:65107200-65120400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr11:65107200-65120600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:65107400-65120400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:65107400-65120400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr11:65107400-65120400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:65107400-65120800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:65107400-65121000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:65107400-65121200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:65107600-65120400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr11:65107600-65120400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:65107600-65120400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr11:65107600-65120400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:65107600-65120400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr11:65107600-65120400	Strong transcription	Placenta	Placenta
47	chr11:65107600-65120400	Strong transcription	Lung	lung
48	chr11:65107600-65120400	Strong transcription	Pancreas	Pancrea
49	chr11:65107600-65120400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr11:65107600-65120400	Strong transcription	Right Ventricle	heart

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