Variant report

Variant	rs3112229
Chromosome Location	chr2:95838674-95838675
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:95830601..95833036-chr2:95838548..95842830,3	K562	blood:
2	chr2:95828222..95833713-chr2:95836399..95844526,15	MCF-7	breast:
3	chr2:95833606..95836006-chr2:95838659..95840200,2	K562	blood:
4	chr2:95807568..95810120-chr2:95838335..95841142,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163067	Chromatin interaction
ENSG00000144026	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10195614	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1104775	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11164122	0.81[CEU][hapmap]
rs11897976	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs12992066	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1559483	0.81[CEU][hapmap]
rs17119148	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1862897	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs1875402	0.85[CEU][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1966272	0.93[EUR][1000 genomes]
rs2001254	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2010533	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2042477	0.85[CEU][hapmap]
rs2098768	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2113417	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs2320339	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2320619	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2320620	0.84[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2320621	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2320624	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3105100	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3105101	0.85[CEU][hapmap];0.84[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3105102	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3105104	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];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3105105	0.90[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];0.97[ASN][1000 genomes]
rs3112221	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112222	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3112223	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112225	0.85[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112228	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	0.85[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112231	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112982	0.80[CEU][hapmap];0.81[AMR][1000 genomes]
rs3112983	0.80[CEU][hapmap]
rs3112984	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112985	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]
rs3112986	0.90[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112987	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112990	0.82[ASN][1000 genomes]
rs3112995	0.85[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112996	0.85[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112997	0.85[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112999	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3113000	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113001	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3755520	0.81[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs3755523	0.81[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs3755525	0.81[CEU][hapmap]
rs3772031	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs3772032	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs3772033	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs3772041	0.81[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs3772042	0.81[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs3772043	0.81[CEU][hapmap]
rs3772044	0.80[CEU][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs3821341	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs4241315	0.91[GIH][hapmap];0.84[TSI][hapmap]
rs4854241	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs4854243	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4854244	0.81[EUR][1000 genomes]
rs4854247	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4854249	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6577012	0.81[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs6577013	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs6715813	0.81[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs6719098	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6723333	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6725821	0.85[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6741001	0.85[CEU][hapmap]
rs6750542	0.85[CEU][hapmap]
rs7565772	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs7574862	0.81[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs7580685	0.81[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs7582368	0.80[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs7585473	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7585914	0.97[CHD][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs7586229	0.82[EUR][1000 genomes]
rs7594144	0.82[CEU][hapmap]
rs870393	0.80[GIH][hapmap];0.88[TSI][hapmap]
rs872580	0.80[CEU][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs889851	0.81[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs889852	0.81[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs889853	0.81[CEU][hapmap]
rs918811	0.85[CEU][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs9678800	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs9989786	0.80[CEU][hapmap];0.80[GIH][hapmap];0.88[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

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95832200-95841000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:95832200-95843200	Weak transcription	Esophagus	oesophagus
3	chr2:95832200-95843200	Weak transcription	Left Ventricle	heart
4	chr2:95832200-95845200	Weak transcription	Placenta	Placenta
5	chr2:95832400-95841600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:95832400-95841800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:95832400-95841800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:95832400-95841800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:95832400-95841800	Weak transcription	Right Ventricle	heart
10	chr2:95832400-95842000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:95832400-95842200	Weak transcription	Osteobl	bone
12	chr2:95832400-95843000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:95832400-95843400	Weak transcription	Psoas Muscle	Psoas
14	chr2:95832400-95845200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:95832400-95845200	Weak transcription	Colonic Mucosa	Colon
16	chr2:95832400-95845400	Weak transcription	Pancreas	Pancrea
17	chr2:95832400-95845600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:95832400-95846400	Weak transcription	Fetal Brain Male	brain
19	chr2:95832400-95846800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:95832600-95841400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:95832600-95841400	Weak transcription	Fetal Lung	lung
22	chr2:95832600-95841800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:95832600-95841800	Weak transcription	Adipose Nuclei	Adipose
24	chr2:95832600-95841800	Weak transcription	Fetal Intestine Large	intestine
25	chr2:95832600-95841800	Weak transcription	Fetal Stomach	stomach
26	chr2:95832600-95842000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:95832600-95842000	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:95832600-95842200	Weak transcription	Primary B cells from cord blood	blood
29	chr2:95832600-95842200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:95832600-95843200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:95832600-95843200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:95832600-95843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:95832600-95843400	Weak transcription	Fetal Intestine Small	intestine
34	chr2:95832600-95843600	Weak transcription	Fetal Brain Female	brain
35	chr2:95832600-95843800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr2:95832600-95844000	Weak transcription	Small Intestine	intestine
37	chr2:95832600-95844400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:95832600-95845000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:95832600-95845200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:95832600-95845200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:95832600-95845200	Weak transcription	HSMM	muscle
42	chr2:95832600-95845400	Weak transcription	Brain Germinal Matrix	brain
43	chr2:95832600-95845600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:95832600-95845600	Weak transcription	Fetal Thymus	thymus
45	chr2:95832600-95846600	Weak transcription	NHDF-Ad	bronchial
46	chr2:95832600-95847000	Weak transcription	K562	blood
47	chr2:95832800-95841200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:95832800-95841400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:95832800-95841600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:95832800-95841600	Weak transcription	Stomach Smooth Muscle	stomach

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