Variant report

Variant	rs2642184
Chromosome Location	chr1:84567765-84567766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84536131..84538617-chr1:84567747..84570815,3	K562	blood:
2	chr1:78469054..78471731-chr1:84565810..84568656,2	K562	blood:
3	chr1:84541330..84545077-chr1:84567686..84570781,4	K562	blood:
4	chr1:84559252..84561971-chr1:84565558..84569310,4	K562	blood:

Variant related genes	Relation type
ENSG00000142875	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000271576	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1016379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031206	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036564	0.85[CEU][hapmap]
rs2139931	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221360	0.81[EUR][1000 genomes]
rs2642181	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642182	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642183	1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs2642185	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2684911	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684916	0.92[EUR][1000 genomes]
rs2811998	0.92[EUR][1000 genomes]
rs2811999	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812001	0.92[EUR][1000 genomes]
rs2812447	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2812451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812452	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2812453	0.96[EUR][1000 genomes]
rs512737	0.81[CHB][hapmap];0.82[YRI][hapmap]
rs626376	0.87[ASW][hapmap];0.86[CHD][hapmap];0.85[YRI][hapmap]
rs663521	0.82[ASN][1000 genomes]
rs667304	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs680905	0.86[CHD][hapmap]
rs72710880	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72710887	0.81[EUR][1000 genomes]
rs72711180	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530801	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs810915	0.86[CHD][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	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv546690	chr1:84562265-84655238	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84545000-84570000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:84545200-84568600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:84545800-84568600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:84552200-84569000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:84555400-84568400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:84556400-84568400	Weak transcription	Brain Angular Gyrus	brain
7	chr1:84556400-84568400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:84556400-84568400	Weak transcription	A549	lung
9	chr1:84556400-84568400	Weak transcription	HSMM	muscle
10	chr1:84556400-84569000	Weak transcription	Left Ventricle	heart
11	chr1:84556600-84568600	Weak transcription	Brain Substantia Nigra	brain
12	chr1:84561000-84568600	Weak transcription	Fetal Lung	lung
13	chr1:84562200-84568800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:84562400-84568400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:84563800-84569000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:84565800-84568000	Enhancers	Fetal Intestine Large	intestine
17	chr1:84566600-84567800	Enhancers	Fetal Intestine Small	intestine
18	chr1:84566600-84568600	Enhancers	K562	blood
19	chr1:84567000-84568600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:84567000-84568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:84567200-84568400	Weak transcription	Hela-S3	cervix
22	chr1:84567200-84568600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:84567200-84568600	Weak transcription	HMEC	breast
24	chr1:84567400-84567800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:84567400-84568400	Weak transcription	NHEK	skin
26	chr1:84567400-84568600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:84567400-84568600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:84567400-84568600	Weak transcription	Stomach Mucosa	stomach

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