Variant report

Variant	rs3755525
Chromosome Location	chr2:95962548-95962549
allele	C/G
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	POLR2A	chr2:95961609-95962628	MCF10A-Er-Src	breast:	n/a	n/a

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	chr2:95830665..95832278-chr2:95962096..95964714,2	MCF-7	breast:
5	chr2:95829346..95831231-chr2:95961091..95963572,2	MCF-7	breast:

Variant related genes	Relation type
KCNIP3	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000144026	Chromatin interaction
ENSG00000163067	Chromatin interaction
ENSG00000155066	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10195614	0.95[EUR][1000 genomes]
rs1104775	0.91[EUR][1000 genomes]
rs11164122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11897976	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12992066	0.89[EUR][1000 genomes]
rs1559483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17119148	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1862897	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1875402	0.86[CEU][hapmap]
rs1966272	0.84[EUR][1000 genomes]
rs2042477	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2098768	0.84[EUR][1000 genomes]
rs2113417	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278065	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2320339	0.93[EUR][1000 genomes]
rs2320624	0.80[EUR][1000 genomes]
rs3105104	0.86[CEU][hapmap]
rs3105105	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs3112225	0.87[CEU][hapmap]
rs3112228	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs3112229	0.81[CEU][hapmap]
rs3112230	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs3112995	0.87[CEU][hapmap]
rs3112996	0.86[CEU][hapmap]
rs3112997	0.86[CEU][hapmap]
rs3113000	0.80[EUR][1000 genomes]
rs3113001	0.80[EUR][1000 genomes]
rs3755518	0.86[AFR][1000 genomes]
rs3755519	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755521	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755526	0.86[EUR][1000 genomes]
rs3772031	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3772032	0.86[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3772033	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3772034	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3772037	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3772041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3772043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772044	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821341	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4283455	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4854247	0.82[EUR][1000 genomes]
rs4854249	0.85[EUR][1000 genomes]
rs4854251	0.80[AFR][1000 genomes]
rs6577012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6577013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6719098	0.82[EUR][1000 genomes]
rs6725821	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs6741001	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6750542	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7574862	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7580685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7585914	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs7586229	0.91[EUR][1000 genomes]
rs7594144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7602807	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs869185	0.82[AFR][1000 genomes]
rs870393	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs889851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs889852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs889853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs918811	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9678800	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9989786	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][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
rs3755525	KCNIP3	cis	Thyroid	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95954400-95962600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:95956400-95965800	Weak transcription	Esophagus	oesophagus
3	chr2:95958200-95963000	Enhancers	Pancreas	Pancrea
4	chr2:95959600-95962800	Weak transcription	Right Atrium	heart
5	chr2:95960000-95973000	Enhancers	Fetal Brain Male	brain
6	chr2:95960800-95962800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:95961200-95962800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr2:95961400-95963000	Enhancers	Fetal Muscle Leg	muscle
9	chr2:95961600-95962600	Enhancers	Brain Substantia Nigra	brain
10	chr2:95961600-95963000	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr2:95961600-95965000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:95961800-95962800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:95961800-95963400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
14	chr2:95961800-95963600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:95962000-95962600	Enhancers	Colon Smooth Muscle	Colon
16	chr2:95962000-95962800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:95962000-95962800	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr2:95962000-95962800	Flanking Active TSS	Fetal Brain Female	brain
19	chr2:95962000-95962800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr2:95962000-95962800	Enhancers	Fetal Stomach	stomach
21	chr2:95962000-95962800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
22	chr2:95962000-95963800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:95962200-95962600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:95962200-95962600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:95962200-95962800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:95962200-95962800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:95962200-95962800	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:95962200-95963000	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr2:95962200-95963000	Enhancers	Gastric	stomach
30	chr2:95962200-95963800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:95962200-95963800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:95962200-95963800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr2:95962200-95964000	Enhancers	Fetal Lung	lung
34	chr2:95962400-95962600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr2:95962400-95962600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:95962400-95962600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:95962400-95962600	Bivalent Enhancer	HSMMtube	muscle
38	chr2:95962400-95962800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:95962400-95962800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr2:95962400-95962800	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr2:95962400-95962800	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr2:95962400-95963000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr2:95962400-95963000	Bivalent Enhancer	Placenta	Placenta
44	chr2:95962400-95963400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:95962400-95963800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:95962400-95964600	Flanking Active TSS	Dnd41	blood

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