Variant report

Variant	rs3112228
Chromosome Location	chr2:95835614-95835615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:95826283..95829129-chr2:95833738..95835738,2	K562	blood:
2	chr2:95833606..95836006-chr2:95838659..95840200,2	K562	blood:
3	chr2:95834987..95837433-chr2:95840484..95842616,2	K562	blood:
4	chr2:95832348..95835657-chr2:95871526..95874855,4	MCF-7	breast:
5	chr2:95833553..95835805-chr2:95846574..95849112,2	K562	blood:

Variant related genes	Relation type
ENSG00000233757	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10195614	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1104775	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11164122	0.86[CEU][hapmap]
rs11897976	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs12992066	0.84[EUR][1000 genomes]
rs1559483	0.86[CEU][hapmap]
rs17119148	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1862897	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs1875402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1966272	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2001254	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2010533	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2042477	0.90[CEU][hapmap]
rs2098768	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2113417	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs2291991	0.83[EUR][1000 genomes]
rs2320339	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2320619	0.85[EUR][1000 genomes]
rs2320620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2320621	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2320624	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3105098	0.80[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3105099	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs3105100	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3105101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3105102	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3105104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3105105	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3112221	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112222	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3112223	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3112229	0.85[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3112231	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3112982	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs3112983	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs3112984	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3112985	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]
rs3112986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112987	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112988	0.81[ASN][1000 genomes]
rs3112990	0.85[ASN][1000 genomes]
rs3112995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112999	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113000	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3113001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3113002	1.00[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs3755520	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3755521	0.81[CEU][hapmap]
rs3755523	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3755525	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs3772031	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs3772032	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs3772033	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs3772041	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3772042	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3772043	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs3772044	0.95[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs3821341	0.81[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs4241315	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs4555374	0.81[CEU][hapmap]
rs4854241	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs4854243	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4854244	0.84[EUR][1000 genomes]
rs4854247	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4854249	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6577012	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs6577013	0.86[CEU][hapmap];0.94[TSI][hapmap]
rs6715813	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs6719098	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6723333	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6725821	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6741001	0.90[CEU][hapmap]
rs6750542	0.90[CEU][hapmap]
rs7565772	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs7574862	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs7580685	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs7582368	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap]
rs7585473	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7585914	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7586229	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7594144	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs870393	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs872580	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs889851	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs889852	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs889853	0.86[CEU][hapmap]
rs918811	0.90[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs9678800	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs9989786	0.85[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][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	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
2	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
3	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
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3112228	KCNIP3	cis	cerebellum	SCAN
rs3112228	SRA1	trans	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95832200-95837600	Weak transcription	Aorta	Aorta
2	chr2:95832200-95841000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:95832200-95843200	Weak transcription	Esophagus	oesophagus
4	chr2:95832200-95843200	Weak transcription	Left Ventricle	heart
5	chr2:95832200-95845200	Weak transcription	Placenta	Placenta
6	chr2:95832400-95841600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:95832400-95841800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:95832400-95841800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:95832400-95841800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:95832400-95841800	Weak transcription	Right Ventricle	heart
11	chr2:95832400-95842000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:95832400-95842200	Weak transcription	Osteobl	bone
13	chr2:95832400-95843000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:95832400-95843400	Weak transcription	Psoas Muscle	Psoas
15	chr2:95832400-95845200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:95832400-95845200	Weak transcription	Colonic Mucosa	Colon
17	chr2:95832400-95845400	Weak transcription	Pancreas	Pancrea
18	chr2:95832400-95845600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:95832400-95846400	Weak transcription	Fetal Brain Male	brain
20	chr2:95832400-95846800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:95832600-95835800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:95832600-95837600	Weak transcription	NHLF	lung
23	chr2:95832600-95841400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:95832600-95841400	Weak transcription	Fetal Lung	lung
25	chr2:95832600-95841800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:95832600-95841800	Weak transcription	Adipose Nuclei	Adipose
27	chr2:95832600-95841800	Weak transcription	Fetal Intestine Large	intestine
28	chr2:95832600-95841800	Weak transcription	Fetal Stomach	stomach
29	chr2:95832600-95842000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:95832600-95842000	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:95832600-95842200	Weak transcription	Primary B cells from cord blood	blood
32	chr2:95832600-95842200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:95832600-95843200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:95832600-95843200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:95832600-95843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:95832600-95843400	Weak transcription	Fetal Intestine Small	intestine
37	chr2:95832600-95843600	Weak transcription	Fetal Brain Female	brain
38	chr2:95832600-95843800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr2:95832600-95844000	Weak transcription	Small Intestine	intestine
40	chr2:95832600-95844400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:95832600-95845000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:95832600-95845200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr2:95832600-95845200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:95832600-95845200	Weak transcription	HSMM	muscle
45	chr2:95832600-95845400	Weak transcription	Brain Germinal Matrix	brain
46	chr2:95832600-95845600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:95832600-95845600	Weak transcription	Fetal Thymus	thymus
48	chr2:95832600-95846600	Weak transcription	NHDF-Ad	bronchial
49	chr2:95832600-95847000	Weak transcription	K562	blood
50	chr2:95832800-95837600	Weak transcription	Primary T cells from cord blood	blood

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