Variant report

Variant	rs6754893
Chromosome Location	chr2:38761787-38761788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38760697..38762690-chr2:38978032..38979542,2	K562	blood:
2	chr2:38760428..38762981-chr2:38976976..38979591,3	K562	blood:
3	chr2:38759515..38762169-chr2:38765133..38766792,2	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12614876	1.00[EUR][1000 genomes]
rs12616367	0.83[EUR][1000 genomes]
rs12619629	0.83[EUR][1000 genomes]
rs12621565	0.83[EUR][1000 genomes]
rs12621788	1.00[EUR][1000 genomes]
rs1543881	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17576044	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17603782	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34133986	0.83[EUR][1000 genomes]
rs36024292	0.83[EUR][1000 genomes]
rs3765001	0.83[EUR][1000 genomes]
rs55785223	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55833813	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56956410	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58720388	0.83[EUR][1000 genomes]
rs59065420	0.83[EUR][1000 genomes]
rs72895897	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72905831	0.83[EUR][1000 genomes]
rs72905839	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73929040	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73929052	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7579783	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7584862	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7606515	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38751200-38762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:38755600-38762800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:38755600-38763000	Weak transcription	Esophagus	oesophagus
4	chr2:38755600-38763000	Weak transcription	Pancreas	Pancrea
5	chr2:38756000-38762800	Weak transcription	Right Atrium	heart
6	chr2:38756800-38762800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:38759600-38763000	Enhancers	Primary B cells from peripheral blood	blood
8	chr2:38759600-38763000	Weak transcription	Brain Substantia Nigra	brain
9	chr2:38759800-38763000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:38760400-38763000	Enhancers	K562	blood
11	chr2:38760600-38762000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:38760600-38762200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:38760600-38763200	Weak transcription	Aorta	Aorta
14	chr2:38761000-38762400	Weak transcription	Adipose Nuclei	Adipose
15	chr2:38761000-38762400	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr2:38761000-38762600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:38761000-38762600	Bivalent Enhancer	HepG2	liver
18	chr2:38761000-38763800	Active TSS	Colon Smooth Muscle	Colon
19	chr2:38761400-38762200	Active TSS	Stomach Smooth Muscle	stomach
20	chr2:38761400-38763000	Enhancers	Brain Anterior Caudate	brain
21	chr2:38761600-38762600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:38761600-38763000	Weak transcription	Primary B cells from cord blood	blood
23	chr2:38761600-38763000	Weak transcription	GM12878-XiMat	blood

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