Variant report

Variant	rs12105792
Chromosome Location	chr2:54780553-54780554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54779914..54782319-chr2:54782662..54788670,5	MCF-7	breast:
2	chr2:54771500..54773380-chr2:54779555..54782261,2	MCF-7	breast:
3	chr2:54777010..54778863-chr2:54780329..54781851,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10165490	0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10180713	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1047499	1.00[ASW][hapmap];0.81[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11892788	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11898012	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12104998	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12468469	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12617036	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713260	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13016942	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]
rs13399435	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1367295	1.00[CEU][hapmap];0.80[CHB][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1541854	0.89[EUR][1000 genomes]
rs17344044	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17344072	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521078	1.00[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1802889	0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs1864493	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292356	0.85[EUR][1000 genomes]
rs2292357	0.80[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes]
rs2941586	0.81[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2941587	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2941595	1.00[ASW][hapmap];0.86[CEU][hapmap];0.88[GIH][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];0.81[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2971879	1.00[ASW][hapmap];0.81[CEU][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[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	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4233954	0.84[EUR][1000 genomes]
rs4444573	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4455199	0.89[EUR][1000 genomes]
rs4514917	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4592889	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671221	0.95[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671222	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671225	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671226	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4671945	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671946	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671947	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671949	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671950	0.80[CHB][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs4671951	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671954	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671955	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671956	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[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]
rs4671960	0.83[TSI][hapmap]
rs4671961	0.84[TSI][hapmap]
rs4990319	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545411	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545413	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545414	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545415	0.86[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6545418	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545419	0.95[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545427	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545434	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6704769	0.91[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6706372	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs6724590	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6729826	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731661	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs6732949	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6734658	0.89[EUR][1000 genomes]
rs6735813	0.89[EUR][1000 genomes]
rs6742607	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6746016	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6746306	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6748816	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6761369	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761398	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7563706	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7589236	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7607451	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs907135	0.81[TSI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12105792	EML6	cis	Thyroid	GTEx
rs12105792	SPTBN1	cis	multi-tissue	Pritchard

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	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:54773400-54784000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:54773400-54784000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:54773800-54782200	Weak transcription	Ovary	ovary
7	chr2:54774000-54782400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:54774000-54782400	Weak transcription	Osteobl	bone
9	chr2:54774800-54781800	Weak transcription	Liver	Liver
10	chr2:54774800-54782400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:54775800-54780600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr2:54775800-54782400	Weak transcription	HSMM	muscle
13	chr2:54777000-54782000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:54777200-54783600	Weak transcription	Fetal Stomach	stomach
15	chr2:54777600-54780800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:54777600-54782000	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:54777600-54782200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:54777600-54782800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:54777600-54783600	Weak transcription	Brain Germinal Matrix	brain
20	chr2:54777600-54784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:54777600-54784800	Weak transcription	Aorta	Aorta
22	chr2:54777800-54782200	Weak transcription	Gastric	stomach
23	chr2:54777800-54782600	Weak transcription	Fetal Kidney	kidney
24	chr2:54777800-54784200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:54778000-54780600	Enhancers	Spleen	Spleen
26	chr2:54778000-54782400	Weak transcription	NHLF	lung
27	chr2:54778000-54783400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:54778000-54784200	Weak transcription	Fetal Brain Male	brain
29	chr2:54778200-54783000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:54778200-54783400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:54778600-54781000	Weak transcription	A549	lung
32	chr2:54778600-54781200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:54778600-54781800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:54778600-54781800	Weak transcription	Placenta	Placenta
35	chr2:54778600-54782400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:54778600-54782600	Weak transcription	Esophagus	oesophagus
37	chr2:54778600-54784000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:54778800-54780600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:54778800-54780800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:54778800-54780800	Enhancers	Fetal Heart	heart
41	chr2:54778800-54781000	Weak transcription	Right Atrium	heart
42	chr2:54778800-54781400	Weak transcription	Psoas Muscle	Psoas
43	chr2:54778800-54781800	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:54778800-54782200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:54778800-54782200	Weak transcription	HMEC	breast
46	chr2:54778800-54782400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:54778800-54782400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:54778800-54782600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:54778800-54782600	Weak transcription	NHEK	skin
50	chr2:54778800-54782800	Weak transcription	Stomach Mucosa	stomach

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