Variant report

Variant	rs3112230
Chromosome Location	chr2:95846158-95846159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95819937..95822932-chr2:95845768..95847351,2	MCF-7	breast:
2	chr2:95842139..95845316-chr2:95846030..95848957,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF514-2	chr2:95843525-95846237	ucscGeneNc_uc002sux_1

Variant related genes	Relation type
ENSG00000144026	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10195614	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1104775	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164122	0.86[CEU][hapmap]
rs11897976	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs12992066	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1559483	0.86[CEU][hapmap]
rs17119148	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862897	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs1875402	1.00[CEU][hapmap];0.95[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];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1966272	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2001254	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2010533	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2042477	0.90[CEU][hapmap]
rs2098768	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2113417	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs2291991	0.83[EUR][1000 genomes]
rs2320339	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2320619	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2320620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2320621	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2320624	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
rs3105100	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[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];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3105102	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3105104	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];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3105105	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112221	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112222	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3112223	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112228	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]
rs3112229	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	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3112982	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3112983	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs3112984	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112985	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]
rs3112986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3112987	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112990	0.83[ASN][1000 genomes]
rs3112995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112996	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];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112997	1.00[ASW][hapmap];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];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112999	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3113000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113001	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113002	0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][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]
rs4854241	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs4854243	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4854244	0.84[EUR][1000 genomes]
rs4854247	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4854249	0.89[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	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6723333	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6725821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6741001	0.90[CEU][hapmap]
rs6750542	0.90[CEU][hapmap]
rs7565772	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][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	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7585914	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7586229	0.85[EUR][1000 genomes];0.82[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	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];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
rs3112230	SRA1	trans	parietal	SCAN
rs3112230	KCNIP3	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95832400-95846400	Weak transcription	Fetal Brain Male	brain
2	chr2:95832400-95846800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:95832600-95846600	Weak transcription	NHDF-Ad	bronchial
4	chr2:95832600-95847000	Weak transcription	K562	blood
5	chr2:95832800-95846600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:95832800-95850200	Weak transcription	Hela-S3	cervix
7	chr2:95838000-95846400	Weak transcription	NHLF	lung
8	chr2:95838400-95851400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:95838800-95846400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:95839600-95849400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:95840400-95850200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:95841000-95849000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr2:95841000-95849200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:95841200-95846800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr2:95841200-95850200	Strong transcription	HepG2	liver
16	chr2:95841600-95846600	Strong transcription	Primary T cells from cord blood	blood
17	chr2:95841600-95846800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:95841800-95846400	Strong transcription	Fetal Stomach	stomach
19	chr2:95841800-95846600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:95841800-95846600	Strong transcription	Fetal Muscle Leg	muscle
21	chr2:95841800-95847000	Strong transcription	Adipose Nuclei	Adipose
22	chr2:95841800-95847000	Strong transcription	Fetal Intestine Large	intestine
23	chr2:95841800-95848800	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr2:95841800-95849200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:95841800-95849400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr2:95842000-95846400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:95842000-95846400	Weak transcription	HMEC	breast
28	chr2:95842000-95846600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:95842000-95849000	Strong transcription	Brain Hippocampus Middle	brain
30	chr2:95842200-95846600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:95842200-95846600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:95842200-95849200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:95842600-95846600	Weak transcription	Right Ventricle	heart
34	chr2:95842800-95846600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:95843000-95846400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:95843000-95847000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:95843000-95847200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:95843000-95848200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr2:95843000-95849000	Strong transcription	Brain Anterior Caudate	brain
40	chr2:95843000-95850200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:95843200-95846600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:95843200-95846600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:95843200-95846600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr2:95843200-95847000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:95843200-95848200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:95843200-95849800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:95843200-95850000	ZNF genes & repeats	Liver	Liver
48	chr2:95843400-95846600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:95843400-95846600	Strong transcription	Fetal Intestine Small	intestine
50	chr2:95843400-95847000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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