Variant report

Variant	rs3755526
Chromosome Location	chr2:95961417-95961418
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:62607405..62609560-chr2:95960744..95963528,2	MCF-7	breast:
2	chr2:95960855..95962599-chr2:95964670..95966568,2	MCF-7	breast:
3	chr2:95940517..95944027-chr2:95960761..95967163,11	MCF-7	breast:
4	chr2:95829346..95831231-chr2:95961091..95963572,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144026	Chromatin interaction
ENSG00000155066	Chromatin interaction
ENSG00000163067	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10195614	0.81[EUR][1000 genomes]
rs11164122	0.84[EUR][1000 genomes]
rs1559483	0.84[EUR][1000 genomes]
rs3755519	0.83[EUR][1000 genomes]
rs3755520	0.84[EUR][1000 genomes]
rs3755521	0.84[EUR][1000 genomes]
rs3755523	0.84[EUR][1000 genomes]
rs3755525	0.86[EUR][1000 genomes]
rs3772037	0.83[EUR][1000 genomes]
rs3772041	0.84[EUR][1000 genomes]
rs3772042	0.84[EUR][1000 genomes]
rs3772043	0.86[EUR][1000 genomes]
rs3772044	0.82[EUR][1000 genomes]
rs6577012	0.84[EUR][1000 genomes]
rs6577013	0.84[EUR][1000 genomes]
rs6715813	0.84[EUR][1000 genomes]
rs7574862	0.84[EUR][1000 genomes]
rs7580685	0.84[EUR][1000 genomes]
rs7594144	0.84[EUR][1000 genomes]
rs870393	0.84[EUR][1000 genomes]
rs889851	0.84[EUR][1000 genomes]
rs889852	0.84[EUR][1000 genomes]
rs889853	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1007627	chr2:95878031-95973743	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv535822	chr2:95878031-95973743	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv998370	chr2:95897299-96074071	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535823	chr2:95897299-96074071	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv528011	chr2:95931218-96057011	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1003196	chr2:95935031-95988314	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1010831	chr2:95935648-96074213	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv535824	chr2:95935648-96074213	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv482871	chr2:95936531-96036880	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1010345	chr2:95939355-95988314	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv999838	chr2:95945923-96003473	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3755526	KCNIP3	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95931400-95961600	Weak transcription	Brain Substantia Nigra	brain
2	chr2:95932400-95961600	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:95954400-95962600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:95956400-95962200	Weak transcription	Gastric	stomach
5	chr2:95956400-95965800	Weak transcription	Esophagus	oesophagus
6	chr2:95957800-95962200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:95958200-95963000	Enhancers	Pancreas	Pancrea
8	chr2:95959200-95962000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:95959600-95962800	Weak transcription	Right Atrium	heart
10	chr2:95960000-95962200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:95960000-95962200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:95960000-95973000	Enhancers	Fetal Brain Male	brain
13	chr2:95960400-95962000	Enhancers	Brain Germinal Matrix	brain
14	chr2:95960800-95961600	Enhancers	Brain Anterior Caudate	brain
15	chr2:95960800-95962400	Enhancers	Brain Angular Gyrus	brain
16	chr2:95960800-95962400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr2:95960800-95962800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:95961000-95961600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:95961000-95962000	Enhancers	Fetal Brain Female	brain
20	chr2:95961000-95962400	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:95961200-95962800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:95961400-95961600	Enhancers	Colonic Mucosa	Colon
23	chr2:95961400-95961800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:95961400-95963000	Enhancers	Fetal Muscle Leg	muscle

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