Variant report

Variant	rs3820411
Chromosome Location	chr1:168513346-168513347
allele	A/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:0)
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	chr1:168513310-168513360	AG04449	skin:	fetal
2	chr1:168513310-168513360	HCM	heart:	n/a
3	chr1:168513310-168513360	GM12878	blood:	n/a
4	chr1:168513310-168513360	Jurkat	blood:	n/a
5	chr1:168513310-168513360	HUVEC	blood vessel:	n/a
6	chr1:168513310-168513360	HCT-116	colon:	n/a
7	chr1:168513310-168513360	NT2-D1	testis:	n/a
8	chr1:168513310-168513360	PFSK-1	brain:	n/a
9	chr1:168513310-168513360	HIPEpiC	eye:	n/a
10	chr1:168513310-168513360	HEEpiC	esophagus:	n/a
11	chr1:168513310-168513360	HL-60	blood:	n/a
12	chr1:168513310-168513360	SAEC	small airway:	n/a
13	chr1:168513310-168513360	BJ	skin:	n/a
14	chr1:168513310-168513360	RPTEC	kidney:	n/a
15	chr1:168513310-168513360	HRPEpiC	eye:	n/a
16	chr1:168513310-168513360	HAEpiC	amniotic membrane:	n/a
17	chr1:168513310-168513360	BE2_C	brain:	n/a
18	chr1:168513310-168513360	AG09309	skin:	n/a
19	chr1:168513310-168513360	GM12891	blood:	n/a
20	chr1:168513310-168513360	Hela-S3	cervix:	n/a
21	chr1:168513310-168513360	HEK293	kidney:	embryo
22	chr1:168513310-168513360	U87	brain:	n/a
23	chr1:168513310-168513360	K562	blood:	n/a
24	chr1:168513310-168513360	SK-N-SH	brain:	n/a
25	chr1:168513310-168513360	ProgFib	skin:	n/a
26	chr1:168513310-168513360	SK-N-SH_RA	brain:	n/a
27	chr1:168513310-168513360	AoSMC	blood vessel:	n/a
28	chr1:168513310-168513360	MCF-7	breast:	n/a
29	chr1:168513310-168513360	HCPEpiC	choroid plexus:	n/a
30	chr1:168513310-168513360	HNPCEpiC	eye:	n/a
31	chr1:168513310-168513360	GM19239	blood:	n/a
32	chr1:168513310-168513360	SKMC	muscle:	n/a
33	chr1:168513310-168513360	NHDF-neo	bronchial:	n/a
34	chr1:168513310-168513360	IMR90	lung:	fetal
35	chr1:168513310-168513360	AG09319	gingival:	n/a
36	chr1:168513310-168513360	PANC-1	pancreas:	n/a
37	chr1:168513310-168513360	HCF	heart:	n/a
38	chr1:168513310-168513360	AG04450	lung:	fetal
39	chr1:168513310-168513360	NB4	blood:	n/a
40	chr1:168513310-168513360	HPAEpiC	pulmonary alveolar:	n/a
41	chr1:168513310-168513360	HMEC	breast:	n/a
42	chr1:168513310-168513360	SK-N-MC	brain:	n/a
43	chr1:168513310-168513360	ECC-1	luminal epithelium:	n/a
44	chr1:168513310-168513360	PrEC	prostate:	n/a
45	chr1:168513310-168513360	HepG2	liver:	n/a
46	chr1:168513310-168513360	A549	lung:	n/a
47	chr1:168513310-168513360	AG10803	skin:	n/a
48	chr1:168513310-168513360	GM12892	blood:	n/a
49	chr1:168513310-168513360	Hepatocyte	liver:	n/a
50	chr1:168513310-168513360	HRE	kidney:	n/a

No data

Variant related genes	Relation type
XCL2	CpG island

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1024176	0.82[ASN][1000 genomes]
rs1024177	0.82[ASN][1000 genomes]
rs10918924	0.83[ASN][1000 genomes]
rs10918925	0.81[ASN][1000 genomes]
rs10918926	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1123864	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12021763	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12049040	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12409982	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568619	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1933100	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1933104	0.81[ASN][1000 genomes]
rs1933105	0.82[ASN][1000 genomes]
rs1933109	0.82[ASN][1000 genomes]
rs1933110	0.82[ASN][1000 genomes]
rs1933112	0.83[ASN][1000 genomes]
rs1933114	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1998510	0.88[AMR][1000 genomes]
rs2179500	0.83[ASN][1000 genomes]
rs2223583	0.82[ASN][1000 genomes]
rs34328291	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3820405	0.85[ASN][1000 genomes]
rs3982407	0.88[ASN][1000 genomes]
rs3982408	0.90[ASN][1000 genomes]
rs4656599	0.88[AMR][1000 genomes]
rs4656601	0.87[AMR][1000 genomes]
rs4656605	0.82[ASN][1000 genomes]
rs475361	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7514168	0.81[ASN][1000 genomes]
rs7516427	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7518740	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7518803	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7543171	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014626	chr1:168441288-168642731	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535196	chr1:168441288-168642731	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1011821	chr1:168441488-168642592	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv535197	chr1:168441488-168642592	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1008852	chr1:168449940-168643905	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv535198	chr1:168449940-168643905	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv946493	chr1:168510865-168514616	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168512400-168513400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr1:168512600-168514400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr1:168513000-168513400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr1:168513000-168513400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:168513000-168513400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr1:168513000-168513400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:168513200-168513400	Enhancers	Primary T helper cells fromperipheralblood	blood

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