Variant report

Variant	rs2123983
Chromosome Location	chr2:55639259-55639260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55638580..55640592-chr2:55645857..55648376,2	MCF-7	breast:
2	chr2:55458173..55459835-chr2:55636615..55639548,2	K562	blood:

Variant related genes	Relation type
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10169185	0.89[GIH][hapmap];0.82[MEX][hapmap]
rs10182704	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10184756	0.82[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10195081	0.81[AFR][1000 genomes]
rs10454144	0.88[EUR][1000 genomes]
rs10518764	0.82[LWK][hapmap]
rs11125565	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11125566	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11125568	0.85[JPT][hapmap]
rs11125569	0.87[JPT][hapmap]
rs11125572	0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs12612806	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12617891	1.00[CEU][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12618216	0.91[ASN][1000 genomes]
rs12618795	0.82[CEU][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12623954	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713297	0.83[ASN][1000 genomes]
rs13394864	0.83[YRI][hapmap]
rs13406929	0.82[LWK][hapmap]
rs13416912	0.84[EUR][1000 genomes]
rs1454415	0.99[ASN][1000 genomes]
rs1454419	0.97[ASN][1000 genomes]
rs1454420	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1454423	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1454424	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1545554	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1598163	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs1902056	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1902057	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902058	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902061	0.82[CEU][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs1902062	0.81[ASN][1000 genomes]
rs2045132	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2045133	0.93[EUR][1000 genomes]
rs2045134	0.97[ASN][1000 genomes]
rs2045135	0.99[ASN][1000 genomes]
rs2045136	0.92[ASN][1000 genomes]
rs2219130	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576688	0.85[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2576703	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589057	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589068	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589069	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589070	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589078	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589079	0.90[EUR][1000 genomes]
rs2589104	0.90[EUR][1000 genomes]
rs2864831	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2864832	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2867173	0.90[EUR][1000 genomes]
rs2867178	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867179	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867194	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2902857	1.00[CEU][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2903507	0.93[EUR][1000 genomes]
rs2903509	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2903514	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2917777	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2920963	0.86[CEU][hapmap]
rs2920970	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2966466	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3099080	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3099081	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3099083	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3111408	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3111409	0.95[EUR][1000 genomes]
rs3748943	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762511	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3974263	0.90[EUR][1000 genomes]
rs4233960	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4233961	1.00[CEU][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs4277563	0.99[ASN][1000 genomes]
rs4481025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535081	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672032	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672033	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672035	0.94[GIH][hapmap];0.81[TSI][hapmap]
rs4672036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672040	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs4672041	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4672043	0.92[ASN][1000 genomes]
rs4672044	0.92[ASN][1000 genomes]
rs4672045	0.89[GIH][hapmap];0.82[MEX][hapmap]
rs59634508	0.90[EUR][1000 genomes]
rs61157332	0.90[EUR][1000 genomes]
rs6545485	0.82[LWK][hapmap]
rs6545486	0.82[LWK][hapmap]
rs6545489	0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545490	1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545492	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6707774	0.82[LWK][hapmap]
rs6709204	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710192	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6718031	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6718909	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6720698	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6721593	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6724840	0.82[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6725968	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6729490	0.83[AFR][1000 genomes]
rs6732633	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6732759	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733814	0.99[ASN][1000 genomes]
rs6744426	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6746757	0.82[LWK][hapmap]
rs6746983	0.82[LWK][hapmap]
rs6748979	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6759625	0.82[LWK][hapmap]
rs72924907	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7424286	0.95[ASN][1000 genomes]
rs7557555	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7557956	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7559987	0.87[JPT][hapmap]
rs7579037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7586440	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7601588	1.00[CEU][hapmap];0.94[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7602189	0.99[ASN][1000 genomes]
rs7606361	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2123983	SPTBN1	cis	cerebellum	SCAN
rs2123983	FLJ31438	cis	multi-tissue	Pritchard

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
3	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
4	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
5	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
8	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
10	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
11	chr2:55624400-55645600	Weak transcription	Ovary	ovary
12	chr2:55628600-55646000	Weak transcription	Esophagus	oesophagus
13	chr2:55630400-55645800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:55630600-55644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:55630800-55642400	Weak transcription	Pancreas	Pancrea
16	chr2:55630800-55644800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:55630800-55645200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:55630800-55645200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:55631000-55645400	Weak transcription	Placenta	Placenta
20	chr2:55631200-55642600	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:55631400-55642600	Weak transcription	Right Ventricle	heart
22	chr2:55631800-55645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:55632000-55644800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:55632600-55645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:55632800-55640000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:55632800-55645800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:55633000-55639400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:55633000-55645000	Weak transcription	Liver	Liver
29	chr2:55633000-55645800	Weak transcription	Fetal Intestine Small	intestine
30	chr2:55633000-55645800	Weak transcription	Spleen	Spleen
31	chr2:55633000-55646000	Weak transcription	Lung	lung
32	chr2:55633200-55639400	Weak transcription	Adipose Nuclei	Adipose
33	chr2:55633200-55639400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:55633200-55644800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:55633400-55639400	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:55633800-55639400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:55633800-55639400	Weak transcription	Left Ventricle	heart
38	chr2:55635400-55639600	Enhancers	Brain Angular Gyrus	brain
39	chr2:55636200-55644200	Weak transcription	Fetal Heart	heart
40	chr2:55636400-55642400	Weak transcription	Fetal Brain Female	brain
41	chr2:55636400-55642600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:55636600-55640200	Weak transcription	NHDF-Ad	bronchial
43	chr2:55636600-55641000	Strong transcription	Fetal Thymus	thymus
44	chr2:55636600-55643200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:55636600-55644000	Weak transcription	HSMMtube	muscle
46	chr2:55636800-55639400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:55636800-55639400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:55636800-55639400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:55636800-55639400	Weak transcription	HSMM	muscle
50	chr2:55636800-55640400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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