Variant report

Variant	rs12104998
Chromosome Location	chr2:54762736-54762737
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54761550..54763887-chr2:54765151..54767469,2	K562	blood:
2	chr2:54760402..54763033-chr2:54763448..54765136,2	MCF-7	breast:
3	chr2:54761267..54763626-chr2:54824184..54826863,2	K562	blood:
4	chr2:54761132..54763342-chr2:54783145..54786144,3	MCF-7	breast:
5	chr2:54761029..54763821-chr2:54783036..54786331,4	K562	blood:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10165490	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs10180713	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs1047499	0.81[CEU][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs11892788	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11898012	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12105792	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	0.87[EUR][1000 genomes]
rs12468469	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12617036	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713260	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13016942	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]
rs13399435	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1367295	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1541854	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17344044	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17344072	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17521078	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1802889	0.80[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1864493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292356	0.84[EUR][1000 genomes]
rs2941586	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs2941587	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs2941595	0.86[CEU][hapmap];0.88[GIH][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2971877	0.81[CEU][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2971879	0.81[CEU][hapmap];0.92[GIH][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2971887	0.86[EUR][1000 genomes]
rs354231	0.84[CEU][hapmap]
rs3796014	0.87[EUR][1000 genomes]
rs4233952	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4233954	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4444573	0.89[EUR][1000 genomes]
rs4455199	0.89[EUR][1000 genomes]
rs4514917	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4519562	0.87[EUR][1000 genomes]
rs4592889	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671221	0.95[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671222	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671225	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671226	0.95[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671945	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671946	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671947	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671949	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671950	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs4671951	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671954	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671955	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671956	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]
rs4671960	0.83[TSI][hapmap]
rs4671961	0.83[TSI][hapmap]
rs4990319	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545411	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545413	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545414	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545415	0.86[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6545418	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545419	0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545427	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545429	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545434	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs6704769	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6706372	0.81[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs6724590	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6729826	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731661	0.86[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6732949	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs6734658	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6735813	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6742607	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6746016	0.91[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6746306	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6748816	0.87[EUR][1000 genomes]
rs6761369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761398	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558950	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7563706	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7589236	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7607451	0.81[CEU][hapmap];1.00[YRI][hapmap];0.88[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	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12104998	EML6	cis	Thyroid	GTEx
rs12104998	SPTBN1	cis	multi-tissue	Pritchard

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
4	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
7	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:54752000-54764600	Weak transcription	Gastric	stomach
9	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:54753800-54764800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:54755000-54767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:54756600-54764200	Weak transcription	Psoas Muscle	Psoas
17	chr2:54756800-54763200	Enhancers	Fetal Intestine Large	intestine
18	chr2:54756800-54767600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:54757000-54767800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
21	chr2:54757400-54766200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:54757400-54771000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
24	chr2:54758600-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:54759400-54763000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr2:54759600-54763800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr2:54759600-54764000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr2:54760200-54768800	Genic enhancers	Left Ventricle	heart
29	chr2:54760400-54764000	Weak transcription	Ovary	ovary
30	chr2:54760400-54769600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:54760600-54762800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:54760600-54763000	Enhancers	Brain Cingulate Gyrus	brain
33	chr2:54760600-54763600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr2:54760600-54763600	Strong transcription	HSMMtube	muscle
35	chr2:54760600-54765200	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:54760600-54766000	Weak transcription	Small Intestine	intestine
37	chr2:54760600-54767000	Weak transcription	NH-A	brain
38	chr2:54760800-54763000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr2:54760800-54763000	Genic enhancers	A549	lung
40	chr2:54760800-54763200	Genic enhancers	HepG2	liver
41	chr2:54760800-54764000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:54760800-54767800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:54761000-54763200	Genic enhancers	Fetal Intestine Small	intestine
44	chr2:54761000-54763400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:54761000-54763400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:54761000-54764800	Strong transcription	Fetal Stomach	stomach
47	chr2:54761000-54767000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:54761000-54769400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:54761200-54763000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:54761200-54764000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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