Variant report

Variant	rs1977578
Chromosome Location	chr6:131306828-131306829
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	chr6:131304583..131308500-chr6:131310186..131313138,4	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006655	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1334689	0.82[CEU][hapmap]
rs1412540	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1984054	0.86[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1999474	0.82[CEU][hapmap]
rs2105250	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs2327005	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4897475	0.82[CEU][hapmap]
rs4897479	0.86[EUR][1000 genomes]
rs6569716	0.81[EUR][1000 genomes]
rs6902768	0.86[EUR][1000 genomes]
rs6920493	0.81[EUR][1000 genomes]
rs6932317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7746714	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7756269	0.81[EUR][1000 genomes]
rs7761655	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7766505	0.82[CEU][hapmap]
rs9375786	0.87[CEU][hapmap]
rs9388870	0.82[CEU][hapmap]
rs9388871	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs9388877	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs9402304	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs9402305	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs9402307	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9402312	0.80[EUR][1000 genomes]
rs946348	0.82[EUR][1000 genomes]
rs9483203	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483204	0.83[LWK][hapmap]
rs9492754	0.82[YRI][hapmap]
rs9492764	0.82[CEU][hapmap]
rs966825	0.81[EUR][1000 genomes]
rs9885632	0.82[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1977578	THEMIS	cis	cerebellum	SCAN
rs1977578	TAAR1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131298800-131314800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:131299000-131309800	Weak transcription	HepG2	liver
3	chr6:131300400-131312200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:131300400-131314600	Weak transcription	Small Intestine	intestine
5	chr6:131303800-131315400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:131304000-131312600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:131304200-131313400	Weak transcription	K562	blood
8	chr6:131304400-131312200	Weak transcription	Fetal Stomach	stomach
9	chr6:131305600-131307000	ZNF genes & repeats	GM12878-XiMat	blood
10	chr6:131305800-131309600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:131306200-131307200	ZNF genes & repeats	Dnd41	blood
12	chr6:131306400-131307000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr6:131306600-131307400	Enhancers	Colon Smooth Muscle	Colon
14	chr6:131306800-131307200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:131306800-131307400	Weak transcription	Thymus	Thymus
16	chr6:131306800-131308400	Weak transcription	Brain Substantia Nigra	brain
17	chr6:131306800-131312200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:131306800-131313800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:131306800-131313800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:131306800-131315200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:131306800-131317000	Weak transcription	Fetal Intestine Small	intestine
22	chr6:131306800-131317200	Weak transcription	NHLF	lung
23	chr6:131306800-131317400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:131306800-131320000	Weak transcription	Left Ventricle	heart

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