Variant report

Variant	rs6545419
Chromosome Location	chr2:54739266-54739267
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:54739200-54739350	HBMEC	blood vessel:	n/a	n/a
2	CTCF	chr2:54739160-54739310	WERI-Rb-1	eye:	n/a	n/a
3	CTCF	chr2:54739180-54739330	HepG2	liver:	n/a	n/a
4	CTCF	chr2:54739160-54739310	GM06990	blood:	n/a	n/a
5	CTCF	chr2:54739177-54739297	K562	blood:	n/a	n/a
6	CTCF	chr2:54739200-54739272	MCF-7	breast:	n/a	n/a
7	CTCF	chr2:54739209-54739268	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
SPTBN1	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10165490	0.80[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs10180713	0.82[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1047499	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs11892788	0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11898012	0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs12104998	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]
rs12105792	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]
rs12467581	0.83[EUR][1000 genomes]
rs12468469	0.84[EUR][1000 genomes]
rs12617036	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713260	0.84[EUR][1000 genomes]
rs13016942	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]
rs13399435	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1367295	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1541854	0.84[EUR][1000 genomes]
rs17344044	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs17344072	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17521078	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1802889	0.82[JPT][hapmap]
rs1864493	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2941586	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs2941587	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs2941595	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2971877	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs2971879	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs2971887	0.81[EUR][1000 genomes]
rs354231	0.84[CEU][hapmap]
rs3796014	0.83[EUR][1000 genomes]
rs4233952	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4233954	0.80[EUR][1000 genomes]
rs4444573	0.85[EUR][1000 genomes]
rs4455199	0.84[EUR][1000 genomes]
rs4514917	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4519562	0.83[EUR][1000 genomes]
rs4592889	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671221	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671222	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671225	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671226	0.91[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4671945	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671946	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671947	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671949	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671950	0.85[JPT][hapmap]
rs4671951	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671954	0.82[ASN][1000 genomes]
rs4671955	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671956	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]
rs4990319	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545411	0.91[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545413	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545414	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545415	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545418	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545420	0.83[EUR][1000 genomes]
rs6545421	0.80[EUR][1000 genomes]
rs6545427	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545429	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545434	0.86[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs6704769	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6706372	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6724590	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6729826	0.91[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6731661	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6732949	0.82[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6734658	0.84[EUR][1000 genomes]
rs6735813	0.83[EUR][1000 genomes]
rs6742607	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6746016	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6746306	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6748816	0.83[EUR][1000 genomes]
rs6761369	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6761398	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7558950	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7563706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7589236	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7607451	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs907135	0.82[CEU][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	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545419	EML6	cis	Thyroid	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54726400-54740000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:54726400-54740000	Weak transcription	Pancreas	Pancrea
4	chr2:54730000-54739400	Weak transcription	Fetal Brain Female	brain
5	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:54730600-54739400	Weak transcription	HepG2	liver
7	chr2:54730600-54740000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:54732800-54740000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
10	chr2:54733000-54743800	Weak transcription	Small Intestine	intestine
11	chr2:54733600-54747000	Weak transcription	Gastric	stomach
12	chr2:54733800-54742200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:54734600-54740800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:54735200-54740400	Enhancers	Left Ventricle	heart
15	chr2:54735600-54740800	Enhancers	Brain Angular Gyrus	brain
16	chr2:54735800-54740600	Enhancers	Brain Hippocampus Middle	brain
17	chr2:54735800-54741000	Enhancers	Brain Substantia Nigra	brain
18	chr2:54736600-54740800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
20	chr2:54737600-54743200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
22	chr2:54737800-54739800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:54738200-54739400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:54738200-54739800	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:54738200-54739800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:54738200-54740000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:54738200-54740000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:54738200-54740000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:54738200-54740000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:54738200-54740000	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:54738200-54740000	Weak transcription	HSMM	muscle
32	chr2:54738200-54740000	Weak transcription	Osteobl	bone
33	chr2:54738200-54740200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:54738200-54743200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:54738200-54743800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:54738200-54746200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:54738200-54746400	Weak transcription	NHLF	lung
38	chr2:54738200-54748200	Weak transcription	Fetal Stomach	stomach
39	chr2:54738200-54751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:54738400-54739400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:54738400-54740000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:54738400-54740000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:54738400-54740000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:54738400-54740000	Weak transcription	Placenta	Placenta
45	chr2:54738400-54740000	Weak transcription	NHDF-Ad	bronchial
46	chr2:54738400-54740400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:54738400-54743200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:54738400-54743400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:54738400-54746200	Weak transcription	A549	lung
50	chr2:54738400-54751400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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