Variant report

Variant	rs35862955
Chromosome Location	chr3:75955760-75955761
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	CTCF	chr3:75955729-75955960	IMR90	lung:	n/a	chr3:75955887-75955900
2	CTCF	chr3:75955760-75955910	WI-38	lung:	n/a	chr3:75955887-75955900
3	POLR2A	chr3:75955719-75955813	MCF-7	breast:	n/a	n/a
4	CTCF	chr3:75955707-75955899	K562	blood:	n/a	n/a
5	CTCF	chr3:75955590-75956027	SK-N-SH	brain:	n/a	chr3:75955887-75955900
6	RAD21	chr3:75955641-75956025	H1-hESC	embryonic stem cell:	n/a	chr3:75955879-75955893
7	ZNF263	chr3:75955451-75956121	HEK293-T-REx	kidney:	n/a	chr3:75955849-75955870
8	POLR2A	chr3:75955734-75956155	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:75955700-75955850	HCFaa	heart:	n/a	n/a
10	CTCF	chr3:75955737-75955991	MCF-7	breast:	n/a	chr3:75955887-75955900
11	CTBP2	chr3:75955733-75956447	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr3:75955720-75956010	WI-38	lung:	n/a	chr3:75955887-75955900
13	SIN3A	chr3:75955749-75956112	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr3:75955709-75955990	Fibrobl	skin:	n/a	chr3:75955887-75955900
15	CTCF	chr3:75955745-75956011	MCF-7	breast:	n/a	chr3:75955887-75955900
16	TBP	chr3:75955690-75956282	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:75955739-75955800	MCF-7	breast:	n/a	n/a
18	TAF1	chr3:75955677-75956190	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr3:75955719-75956023	NHEK	skin:	n/a	chr3:75955887-75955900
20	TEAD4	chr3:75955694-75956108	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr3:75955741-75956007	ProgFib	skin:	n/a	chr3:75955887-75955900
22	RAD21	chr3:75955675-75955981	SK-N-SH_RA	brain:	n/a	chr3:75955879-75955893
23	CTCF	chr3:75955672-75956077	H1-hESC	embryonic stem cell:	n/a	chr3:75955887-75955900
24	CTCF	chr3:75955700-75955850	HAc	cerebellar:	n/a	n/a
25	MXI1	chr3:75955709-75955900	H1-hESC	embryonic stem cell:	n/a	n/a
26	BACH1	chr3:75955701-75956187	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr3:75955713-75956030	H1-hESC	embryonic stem cell:	n/a	chr3:75955887-75955900
28	RAD21	chr3:75955737-75956046	H1-hESC	embryonic stem cell:	n/a	chr3:75955879-75955893
29	MAX	chr3:75955664-75956073	H1-hESC	embryonic stem cell:	n/a	chr3:75955773-75955782
30	YY1	chr3:75955738-75956077	H1-hESC	embryonic stem cell:	n/a	n/a
31	RAD21	chr3:75955602-75956180	H1-hESC	embryonic stem cell:	n/a	chr3:75955879-75955893
32	POLR2A	chr3:75955731-75956076	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr3:75955738-75955941	SK-N-SH_RA	brain:	n/a	chr3:75955879-75955893
34	MAX	chr3:75955659-75956100	H1-hESC	embryonic stem cell:	n/a	chr3:75955773-75955782
35	POLR2A	chr3:75955662-75956424	H1-hESC	embryonic stem cell:	n/a	n/a
36	CHD2	chr3:75955746-75956057	H1-hESC	embryonic stem cell:	n/a	chr3:75955999-75956009
37	JUN	chr3:75955678-75955867	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:75955720-75955870	HAc	cerebellar:	n/a	n/a

Variant related genes	Relation type
ROBO2	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12632783	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13075661	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13078223	0.92[EUR][1000 genomes]
rs715468	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997253	chr3:75168497-76021627	Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
2	esv2756999	chr3:75392078-76003036	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
3	nsv876983	chr3:75572199-76024339	Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv428418	chr3:75615943-75973574	Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
5	esv2757875	chr3:75617595-76077290	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
6	esv2754135	chr3:75713010-76016610	Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
7	nsv876989	chr3:75800666-76029306	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv876990	chr3:75800666-76051624	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv876991	chr3:75800666-76059499	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv876992	chr3:75867951-76029306	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv876993	chr3:75904105-76077143	ZNF genes & repeats Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv876994	chr3:75935763-75976655	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35862955	ZNF717	cis	Thyroid	GTEx
rs35862955	LINC00960	cis	Thyroid	GTEx
rs35862955	LINC00960	cis	Skin Sun Exposed Lower leg	GTEx
rs35862955	LINC00960	cis	Esophagus Mucosa	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:75955400-75955800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:75955400-75955800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:75955400-75955800	Active TSS	Brain Germinal Matrix	brain
4	chr3:75955400-75956400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:75955400-75956400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr3:75955400-75956800	Active TSS	Fetal Brain Male	brain
7	chr3:75955400-75958400	Active TSS	Fetal Brain Female	brain
8	chr3:75955600-75955800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
9	chr3:75955600-75955800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:75955600-75955800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:75955600-75955800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:75955600-75955800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
13	chr3:75955600-75955800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:75955600-75955800	Active TSS	Adipose Nuclei	Adipose
15	chr3:75955600-75955800	Active TSS	Brain Cingulate Gyrus	brain
16	chr3:75955600-75955800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
17	chr3:75955600-75955800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr3:75955600-75955800	Flanking Active TSS	Fetal Muscle Trunk	muscle
19	chr3:75955600-75955800	Active TSS	Fetal Muscle Leg	muscle
20	chr3:75955600-75955800	Active TSS	Fetal Stomach	stomach
21	chr3:75955600-75955800	Enhancers	Pancreas	Pancrea
22	chr3:75955600-75955800	Enhancers	Psoas Muscle	Psoas
23	chr3:75955600-75955800	Bivalent/Poised TSS	Right Ventricle	heart
24	chr3:75955600-75956000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:75955600-75956000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:75955600-75956000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
27	chr3:75955600-75956000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
28	chr3:75955600-75956200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:75955600-75956200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr3:75955600-75956200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:75955600-75956200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:75955600-75956200	Active TSS	Brain Angular Gyrus	brain
33	chr3:75955600-75956200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:75955600-75956200	Active TSS	Brain Substantia Nigra	brain
35	chr3:75955600-75956200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr3:75955600-75956200	Bivalent/Poised TSS	Fetal Lung	lung
37	chr3:75955600-75956200	Enhancers	Ovary	ovary
38	chr3:75955600-75956400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:75955600-75956400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:75955600-75956400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr3:75955600-75956400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:75955600-75956400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr3:75955600-75956400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
44	chr3:75955600-75956600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:75955600-75956600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:75955600-75956600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:75955600-75956600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:75955600-75956600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:75955600-75956600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:75955600-75956600	Active TSS	Fetal Kidney	kidney

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