Variant report

Variant	rs2840584
Chromosome Location	chr1:159925431-159925432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:159925416-159925466	HAEpiC	amniotic membrane:	n/a
2	chr1:159925416-159925466	K562	blood:	n/a
3	chr1:159925416-159925466	AG09319	gingival:	n/a
4	chr1:159925416-159925466	HUVEC	blood vessel:	n/a
5	chr1:159925416-159925466	GM12892	blood:	n/a
6	chr1:159925416-159925466	H1-hESC	embryonic stem cell:	embryo
7	chr1:159925416-159925466	ECC-1	luminal epithelium:	n/a
8	chr1:159925416-159925466	Jurkat	blood:	n/a
9	chr1:159925416-159925466	HEEpiC	esophagus:	n/a
10	chr1:159925416-159925466	HepG2	liver:	n/a
11	chr1:159925416-159925466	T-47D	breast:	n/a
12	chr1:159925416-159925466	MCF10A-Er-Src	breast:	n/a
13	chr1:159925416-159925466	HRE	kidney:	n/a
14	chr1:159925416-159925466	AG04449	skin:	fetal
15	chr1:159925416-159925466	HCF	heart:	n/a
16	chr1:159925416-159925466	SKMC	muscle:	n/a
17	chr1:159925416-159925466	HIPEpiC	eye:	n/a
18	chr1:159925416-159925466	HNPCEpiC	eye:	n/a
19	chr1:159925416-159925466	A549	lung:	n/a
20	chr1:159925416-159925466	NH-A	brain:	n/a
21	chr1:159925416-159925466	IMR90	lung:	fetal
22	chr1:159925416-159925466	NHBE	bronchial:	n/a
23	chr1:159925416-159925466	NB4	blood:	n/a
24	chr1:159925416-159925466	ovcar-3	ovarian:	n/a
25	chr1:159925416-159925466	U87	brain:	n/a
26	chr1:159925416-159925466	LNCaP	prostate:	n/a
27	chr1:159925416-159925466	NT2-D1	testis:	n/a
28	chr1:159925416-159925466	HCM	heart:	n/a
29	chr1:159925416-159925466	AG09309	skin:	n/a
30	chr1:159925416-159925466	SK-N-SH	brain:	n/a
31	chr1:159925416-159925466	HEK293	kidney:	embryo
32	chr1:159925416-159925466	HCT-116	colon:	n/a
33	chr1:159925416-159925466	RPTEC	kidney:	n/a
34	chr1:159925416-159925466	ProgFib	skin:	n/a
35	chr1:159925416-159925466	BJ	skin:	n/a
36	chr1:159925416-159925466	PFSK-1	brain:	n/a
37	chr1:159925416-159925466	SK-N-MC	brain:	n/a
38	chr1:159925416-159925466	PrEC	prostate:	n/a
39	chr1:159925416-159925466	HPAEpiC	pulmonary alveolar:	n/a
40	chr1:159925416-159925466	HCPEpiC	choroid plexus:	n/a
41	chr1:159925416-159925466	NHDF-neo	bronchial:	n/a
42	chr1:159925416-159925466	BE2_C	brain:	n/a
43	chr1:159925416-159925466	SAEC	small airway:	n/a
44	chr1:159925416-159925466	AoSMC	blood vessel:	n/a
45	chr1:159925416-159925466	CMK	blood:	n/a
46	chr1:159925416-159925466	PANC-1	pancreas:	n/a
47	chr1:159925416-159925466	AG10803	skin:	n/a
48	chr1:159925416-159925466	GM12878	blood:	n/a
49	chr1:159925416-159925466	GM19239	blood:	n/a
50	chr1:159925416-159925466	Hepatocyte	liver:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159925103..159927154-chr1:159928753..159930871,2	MCF-7	breast:
2	chr1:159915177..159916048-chr1:159924751..159925565,2	K562	blood:

No data

Variant related genes	Relation type
SLAMF9	CpG island
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1316963	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs1317520	0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2249707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789419	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820555	0.90[EUR][1000 genomes]
rs2840582	0.91[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806199	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs59975218	0.90[ASN][1000 genomes]
rs60669636	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][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	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv548055	chr1:159918418-159940000	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv520773	chr1:159922959-159935569	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
2	chr1:159919800-159930400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:159923000-159926200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:159923400-159926400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:159923400-159926400	Enhancers	NHEK	skin
6	chr1:159923600-159925600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:159924000-159927800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:159924000-159928800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:159924000-159928800	Weak transcription	Esophagus	oesophagus
10	chr1:159924200-159928400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:159924400-159927200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:159924400-159927200	Weak transcription	K562	blood
13	chr1:159924400-159929200	Weak transcription	Osteobl	bone
14	chr1:159925200-159929600	Weak transcription	NHDF-Ad	bronchial
15	chr1:159925400-159929000	Weak transcription	HMEC	breast

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