Variant report

Variant	rs56012560
Chromosome Location	chr1:212993546-212993547
allele	C/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	STAT3	chr1:212993095-212993584	GM12878	blood:	n/a	n/a
2	NFIC	chr1:212992868-212993685	GM12878	blood:	n/a	n/a
3	TCF7L2	chr1:212993212-212993578	HepG2	liver:	n/a	chr1:212993270-212993279

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212986725..212988338-chr1:212992887..212995652,2	K562	blood:
2	chr1:212969236..212971127-chr1:212991811..212994407,2	K562	blood:

Variant related genes	Relation type
ENSG00000236905	TF binding region
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11799556	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11801900	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11804851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807916	1.00[AMR][1000 genomes]
rs17019640	1.00[AMR][1000 genomes]
rs17019657	1.00[AMR][1000 genomes]
rs17019749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17019770	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28505349	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41300963	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55787749	1.00[AMR][1000 genomes]
rs55827218	1.00[AMR][1000 genomes]
rs60334006	1.00[AMR][1000 genomes]
rs6684313	1.00[AMR][1000 genomes]
rs6685348	1.00[AMR][1000 genomes]
rs6700258	1.00[AMR][1000 genomes]
rs74138622	1.00[AMR][1000 genomes]
rs74138623	1.00[AMR][1000 genomes]
rs74138629	1.00[AMR][1000 genomes]
rs74138630	1.00[AMR][1000 genomes]
rs74138631	1.00[AMR][1000 genomes]
rs74138632	1.00[AMR][1000 genomes]
rs74138633	1.00[AMR][1000 genomes]
rs74138636	1.00[AMR][1000 genomes]
rs74138700	1.00[AMR][1000 genomes]
rs74140507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74140511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74140512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74141106	1.00[AMR][1000 genomes]
rs7511916	1.00[AMR][1000 genomes]
rs7523527	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7538679	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7551472	1.00[AMR][1000 genomes]
rs7551969	1.00[AMR][1000 genomes]

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	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
2	chr1:212972400-212993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:212975800-212997800	Weak transcription	Brain Substantia Nigra	brain
4	chr1:212976200-212998800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:212979200-212994200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:212980800-213001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:212988400-212998800	Weak transcription	Adipose Nuclei	Adipose
9	chr1:212988600-212998400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:212988800-212993800	Weak transcription	Fetal Thymus	thymus
11	chr1:212990400-212995600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:212990800-212998600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:212991000-212998800	Weak transcription	Stomach Mucosa	stomach
14	chr1:212992400-212993600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:212992400-212994000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:212992400-212994600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:212992400-212994800	Enhancers	HepG2	liver
18	chr1:212992600-212993600	Enhancers	Fetal Intestine Large	intestine
19	chr1:212992600-212993600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr1:212992600-212994000	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:212992800-212993600	Flanking Active TSS	GM12878-XiMat	blood
22	chr1:212992800-212993800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:212993000-212993600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:212993200-212994000	Enhancers	Primary B cells from cord blood	blood
25	chr1:212993200-212995000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr1:212993400-212994200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:212993400-212994400	Enhancers	Primary hematopoietic stem cells	blood

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