Variant report

Variant	rs10195614
Chromosome Location	chr2:95957777-95957778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:95941675..95944170-chr2:95957167..95960145,2	MCF-7	breast:
2	chr2:95930734..95933146-chr2:95956252..95958672,2	MCF-7	breast:
3	chr2:95924662..95927422-chr2:95957580..95961049,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155066	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1104775	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11164122	0.94[EUR][1000 genomes]
rs11897976	0.91[EUR][1000 genomes]
rs12992066	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1559483	0.94[EUR][1000 genomes]
rs17119148	0.85[EUR][1000 genomes]
rs1862897	0.92[EUR][1000 genomes]
rs1875402	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1966272	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2001254	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2010533	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2042477	0.92[EUR][1000 genomes]
rs2098768	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2113417	0.91[EUR][1000 genomes]
rs2320339	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2320621	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2320624	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3105100	0.81[AMR][1000 genomes]
rs3105102	0.81[EUR][1000 genomes]
rs3105104	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3105105	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112221	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112223	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112225	0.81[AMR][1000 genomes]
rs3112228	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112229	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3112230	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112231	0.86[AMR][1000 genomes]
rs3112995	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112996	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112997	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112999	0.80[EUR][1000 genomes]
rs3113000	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3113001	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3755519	0.93[EUR][1000 genomes]
rs3755520	0.94[EUR][1000 genomes]
rs3755521	0.94[EUR][1000 genomes]
rs3755523	0.94[EUR][1000 genomes]
rs3755525	0.95[EUR][1000 genomes]
rs3755526	0.81[EUR][1000 genomes]
rs3772031	0.92[EUR][1000 genomes]
rs3772032	0.92[EUR][1000 genomes]
rs3772033	0.92[EUR][1000 genomes]
rs3772034	0.88[EUR][1000 genomes]
rs3772037	0.93[EUR][1000 genomes]
rs3772041	0.94[EUR][1000 genomes]
rs3772042	0.94[EUR][1000 genomes]
rs3772043	0.95[EUR][1000 genomes]
rs3772044	0.99[EUR][1000 genomes]
rs3821341	0.89[EUR][1000 genomes]
rs4283455	0.92[EUR][1000 genomes]
rs4854247	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4854249	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6577012	0.94[EUR][1000 genomes]
rs6577013	0.94[EUR][1000 genomes]
rs6715813	0.94[EUR][1000 genomes]
rs6719098	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6725821	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6741001	0.92[EUR][1000 genomes]
rs6750542	0.92[EUR][1000 genomes]
rs7574862	0.94[EUR][1000 genomes]
rs7580685	0.94[EUR][1000 genomes]
rs7585914	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7586229	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7594144	0.94[EUR][1000 genomes]
rs7602807	0.92[EUR][1000 genomes]
rs870393	0.91[EUR][1000 genomes]
rs889851	0.94[EUR][1000 genomes]
rs889852	0.94[EUR][1000 genomes]
rs889853	0.94[EUR][1000 genomes]
rs918811	0.92[EUR][1000 genomes]
rs9678800	0.92[EUR][1000 genomes]
rs9989786	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
16	esv2043868	chr2:95957776-95957778	ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10195614	KCNIP3	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95931400-95961000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:95931400-95961600	Weak transcription	Brain Substantia Nigra	brain
3	chr2:95932400-95961600	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:95945800-95958200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:95946800-95960000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:95947800-95960800	Weak transcription	Brain Angular Gyrus	brain
7	chr2:95954400-95958200	Weak transcription	Pancreas	Pancrea
8	chr2:95954400-95962600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:95954600-95958400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:95955200-95958200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:95955400-95961200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:95956400-95961400	Weak transcription	Stomach Mucosa	stomach
13	chr2:95956400-95962200	Weak transcription	Gastric	stomach
14	chr2:95956400-95965800	Weak transcription	Esophagus	oesophagus
15	chr2:95956600-95958000	Weak transcription	HMEC	breast
16	chr2:95957200-95958200	ZNF genes & repeats	Colonic Mucosa	Colon
17	chr2:95957600-95958000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:95957600-95958000	Weak transcription	NHEK	skin
19	chr2:95957600-95958200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:95957600-95958200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:95957600-95959600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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