Variant report

Variant	rs13016942
Chromosome Location	chr2:54779234-54779235
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	chr2:54777753..54780191-chr2:54782738..54786905,5	K562	blood:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10165490	0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs10180713	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1047499	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11885703	0.81[EUR][1000 genomes]
rs11892788	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11898012	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12104998	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12105792	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12468469	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12617036	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713260	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13399435	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1367295	0.95[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1541854	0.91[EUR][1000 genomes]
rs17344044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17344072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521078	0.95[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1802889	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1864493	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292356	0.86[EUR][1000 genomes]
rs2292357	0.82[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes]
rs2941586	0.86[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2941587	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2941595	1.00[ASW][hapmap];0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2971877	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2971879	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2971883	1.00[AFR][1000 genomes]
rs2971887	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs354231	0.84[CEU][hapmap]
rs354236	0.84[TSI][hapmap]
rs3796014	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4233952	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4233954	0.85[EUR][1000 genomes]
rs4444573	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4455199	0.91[EUR][1000 genomes]
rs4514917	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4592889	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671221	0.90[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671222	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671225	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671226	1.00[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4671945	0.95[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671946	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671947	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671949	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671950	0.80[CHB][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4671951	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671953	0.80[EUR][1000 genomes]
rs4671954	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671955	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs4671960	0.83[TSI][hapmap]
rs4671961	0.84[TSI][hapmap]
rs4990319	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545411	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545413	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545414	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545415	0.91[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545418	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545419	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545420	0.80[EUR][1000 genomes]
rs6545427	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545434	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6704769	0.95[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6706372	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs6724590	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6729826	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731661	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs6732949	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6734658	0.91[EUR][1000 genomes]
rs6735813	0.89[EUR][1000 genomes]
rs6742607	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6746016	0.86[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6746306	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6748816	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6761369	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761398	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7563706	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7589236	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7607451	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs907135	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13016942	NM_020217	cis	multi-tissue	Pritchard
rs13016942	EML6	cis	Thyroid	GTEx
rs13016942	SPTBN1	cis	multi-tissue	Pritchard
rs13016942	RPL23AP32	cis	Liver	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:54770600-54780200	Enhancers	Fetal Intestine Large	intestine
4	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:54772600-54780200	Enhancers	Fetal Intestine Small	intestine
6	chr2:54773400-54784000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:54773400-54784000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:54773800-54782200	Weak transcription	Ovary	ovary
9	chr2:54774000-54782400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:54774000-54782400	Weak transcription	Osteobl	bone
11	chr2:54774200-54779800	Weak transcription	NHDF-Ad	bronchial
12	chr2:54774800-54781800	Weak transcription	Liver	Liver
13	chr2:54774800-54782400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:54775600-54779400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:54775800-54780600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:54775800-54782400	Weak transcription	HSMM	muscle
17	chr2:54776800-54779400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:54776800-54780200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:54776800-54780200	Enhancers	Pancreas	Pancrea
20	chr2:54777000-54780200	Enhancers	Lung	lung
21	chr2:54777000-54782000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:54777200-54783600	Weak transcription	Fetal Stomach	stomach
23	chr2:54777400-54779400	Enhancers	GM12878-XiMat	blood
24	chr2:54777400-54779600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr2:54777600-54780000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:54777600-54780800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:54777600-54782000	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:54777600-54782200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:54777600-54782800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:54777600-54783600	Weak transcription	Brain Germinal Matrix	brain
31	chr2:54777600-54784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:54777600-54784800	Weak transcription	Aorta	Aorta
33	chr2:54777800-54779400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr2:54777800-54780400	Weak transcription	Adipose Nuclei	Adipose
35	chr2:54777800-54782200	Weak transcription	Gastric	stomach
36	chr2:54777800-54782600	Weak transcription	Fetal Kidney	kidney
37	chr2:54777800-54784200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:54778000-54780400	Weak transcription	HSMMtube	muscle
39	chr2:54778000-54780600	Enhancers	Spleen	Spleen
40	chr2:54778000-54782400	Weak transcription	NHLF	lung
41	chr2:54778000-54783400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:54778000-54784200	Weak transcription	Fetal Brain Male	brain
43	chr2:54778200-54779400	Genic enhancers	Left Ventricle	heart
44	chr2:54778200-54783000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:54778200-54783400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:54778400-54779400	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr2:54778400-54780400	Weak transcription	Brain Substantia Nigra	brain
48	chr2:54778600-54779800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr2:54778600-54780000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:54778600-54780200	Weak transcription	Brain Angular Gyrus	brain

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