Variant report

Variant	rs3796012
Chromosome Location	chr2:54843214-54843215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54841576..54843429-chr2:54853374..54855591,2	K562	blood:
2	chr2:54842967..54844485-chr2:54847665..54849553,2	MCF-7	breast:
3	chr2:54837203..54842761-chr2:54843020..54847377,6	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10164713	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1027950	0.83[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1052788	0.85[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs1052820	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs1112919	0.83[CEU][hapmap]
rs12467653	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12473338	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12475342	0.82[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12475598	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12476489	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12615589	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12620195	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17416284	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2007020	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3817163	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4283459	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4519565	0.92[CEU][hapmap]
rs4557016	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4567979	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671223	0.92[CEU][hapmap]
rs4671224	0.92[CEU][hapmap]
rs4671227	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671229	0.83[CEU][hapmap]
rs4671952	0.87[CEU][hapmap]
rs4671959	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671962	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671964	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671966	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59871921	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60294349	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545428	0.84[CEU][hapmap]
rs6545433	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545438	0.87[CHB][hapmap]
rs6705756	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6738725	0.87[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs6739099	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67457439	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72618663	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72618664	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9309255	0.87[CEU][hapmap]

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	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	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
rs3796012	EML6	cis	Artery Tibial	GTEx
rs3796012	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54829800-54859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:54832400-54843400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54832400-54843800	Weak transcription	Brain Germinal Matrix	brain
4	chr2:54833400-54843400	Weak transcription	Fetal Brain Male	brain
5	chr2:54838200-54843400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:54838600-54845600	Strong transcription	GM12878-XiMat	blood
7	chr2:54838800-54843800	Genic enhancers	Brain Hippocampus Middle	brain
8	chr2:54838800-54845800	Strong transcription	Primary B cells from cord blood	blood
9	chr2:54838800-54845800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:54838800-54846200	Enhancers	Right Atrium	heart
11	chr2:54838800-54848800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:54838800-54860200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:54839000-54846800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:54839000-54848200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:54839000-54864200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:54839200-54844600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:54839200-54845000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:54839200-54845200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr2:54839200-54845200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:54839200-54845200	Strong transcription	Fetal Stomach	stomach
22	chr2:54839200-54845400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:54839200-54845400	Strong transcription	Thymus	Thymus
24	chr2:54839200-54845600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:54839200-54845600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:54839200-54845600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:54839200-54845800	Strong transcription	Colonic Mucosa	Colon
28	chr2:54839200-54846800	Genic enhancers	Liver	Liver
29	chr2:54839200-54848600	Genic enhancers	Left Ventricle	heart
30	chr2:54839200-54861800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:54839200-54866000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:54839400-54853000	Strong transcription	Fetal Intestine Large	intestine
33	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:54839600-54845200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr2:54839600-54845200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:54839600-54852400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:54839600-54862600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:54839800-54844200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:54839800-54846800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:54839800-54847200	Genic enhancers	Fetal Lung	lung
41	chr2:54840000-54845400	Strong transcription	Fetal Thymus	thymus
42	chr2:54840800-54843800	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:54840800-54845600	Strong transcription	Dnd41	blood
44	chr2:54840800-54861400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:54841000-54845400	Strong transcription	Placenta	Placenta
46	chr2:54841000-54861400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:54841000-54861400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:54841200-54844200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:54841200-54845400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:54841200-54845600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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