Variant report

Variant	rs3112985
Chromosome Location	chr2:95729053-95729054
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95718897..95720401-chr2:95727310..95730264,2	MCF-7	breast:
2	chr2:95720619..95723205-chr2:95727451..95729974,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231062	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10172167	0.81[CEU][hapmap]
rs17119148	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs1875402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs1966272	0.81[EUR][1000 genomes]
rs2001254	0.85[EUR][1000 genomes]
rs2098768	0.81[EUR][1000 genomes]
rs2291991	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2320619	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2320620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2320621	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2320624	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3105098	0.80[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3105099	0.89[ASW][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap];0.82[ASN][1000 genomes]
rs3105100	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3105101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3105102	0.83[EUR][1000 genomes]
rs3105104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs3105105	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3112221	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112222	0.85[EUR][1000 genomes]
rs3112223	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3112228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112229	0.85[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3112230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3112231	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3112982	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3112983	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3112984	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3112986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112987	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3112988	0.87[ASN][1000 genomes]
rs3112990	0.88[ASN][1000 genomes]
rs3112995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs3112996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs3112997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112999	0.80[EUR][1000 genomes]
rs3113000	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3113001	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3113002	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4241315	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4555374	0.81[CEU][hapmap]
rs4564804	0.81[CEU][hapmap]
rs4854241	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs4854243	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4854244	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4854247	0.83[EUR][1000 genomes]
rs4854249	0.80[EUR][1000 genomes]
rs6708474	0.80[CEU][hapmap]
rs6719098	0.83[EUR][1000 genomes]
rs6723333	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6725821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs7560571	0.81[CHB][hapmap]
rs7565772	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7582368	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs7585473	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs872580	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9324212	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	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
5	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3112985	KCNIP3	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95721600-95729800	Enhancers	Fetal Thymus	thymus
2	chr2:95724400-95729600	Enhancers	Brain Substantia Nigra	brain
3	chr2:95724400-95729800	Enhancers	Brain Cingulate Gyrus	brain
4	chr2:95724400-95729800	Enhancers	Brain Hippocampus Middle	brain
5	chr2:95724400-95729800	Enhancers	Esophagus	oesophagus
6	chr2:95725800-95732000	Weak transcription	Pancreas	Pancrea
7	chr2:95726000-95729600	Enhancers	Brain Angular Gyrus	brain
8	chr2:95726400-95729200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:95726400-95730000	Enhancers	Dnd41	blood
10	chr2:95726600-95729400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:95726600-95729600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr2:95726600-95729600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr2:95726600-95729600	Enhancers	Thymus	Thymus
14	chr2:95726800-95729200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:95726800-95729400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:95726800-95729800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:95726800-95729800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr2:95727000-95729800	Enhancers	Primary T cells from cord blood	blood
19	chr2:95727200-95729600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:95727800-95729600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:95727800-95730000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:95728200-95729200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:95728400-95729200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:95728400-95729200	Enhancers	Stomach Mucosa	stomach
25	chr2:95728400-95729800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:95728600-95729200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:95728600-95729600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:95728600-95729600	Enhancers	Primary B cells from peripheral blood	blood
29	chr2:95729000-95729200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
30	chr2:95729000-95729200	Bivalent Enhancer	HepG2	liver
31	chr2:95729000-95730000	Enhancers	GM12878-XiMat	blood
32	chr2:95729000-95730400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:95729000-95731000	Weak transcription	Brain Anterior Caudate	brain

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