Variant report

Variant	rs35877985
Chromosome Location	chr1:186264721-186264722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:186264684-186264734	BE2_C	brain:	n/a
2	chr1:186264674-186264724	SK-N-MC	brain:	n/a
3	chr1:186264674-186264724	H1-hESC	embryonic stem cell:	embryo
4	chr1:186264684-186264734	GM12892	blood:	n/a
5	chr1:186264684-186264734	H1-hESC	embryonic stem cell:	embryo
6	chr1:186264684-186264734	HCPEpiC	choroid plexus:	n/a
7	chr1:186264674-186264724	ProgFib	skin:	n/a
8	chr1:186264674-186264724	AG09319	gingival:	n/a
9	chr1:186264684-186264734	NH-A	brain:	n/a
10	chr1:186264684-186264734	NB4	blood:	n/a
11	chr1:186264684-186264734	GM06990	blood:	n/a
12	chr1:186264684-186264734	HEEpiC	esophagus:	n/a
13	chr1:186264684-186264734	GM19239	blood:	n/a
14	chr1:186264684-186264734	K562	blood:	n/a
15	chr1:186264674-186264724	PFSK-1	brain:	n/a
16	chr1:186264684-186264734	NHDF-neo	bronchial:	n/a
17	chr1:186264684-186264734	HepG2	liver:	n/a
18	chr1:186264674-186264724	GM12892	blood:	n/a
19	chr1:186264674-186264724	HUVEC	blood vessel:	n/a
20	chr1:186264674-186264724	NHBE	bronchial:	n/a
21	chr1:186264684-186264734	HIPEpiC	eye:	n/a
22	chr1:186264674-186264724	A549	lung:	n/a
23	chr1:186264674-186264724	AG04450	lung:	fetal
24	chr1:186264674-186264724	Caco-2	colon:	n/a
25	chr1:186264684-186264734	AG10803	skin:	n/a
26	chr1:186264674-186264724	RPTEC	kidney:	n/a
27	chr1:186264674-186264724	AG09309	skin:	n/a
28	chr1:186264684-186264734	AG09309	skin:	n/a
29	chr1:186264684-186264734	SAEC	small airway:	n/a
30	chr1:186264684-186264734	PFSK-1	brain:	n/a
31	chr1:186264674-186264724	GM12878	blood:	n/a
32	chr1:186264674-186264724	BJ	skin:	n/a
33	chr1:186264684-186264734	IMR90	lung:	fetal
34	chr1:186264674-186264724	HEK293	kidney:	embryo
35	chr1:186264674-186264724	Jurkat	blood:	n/a
36	chr1:186264674-186264724	HCPEpiC	choroid plexus:	n/a
37	chr1:186264684-186264734	LNCaP	prostate:	n/a
38	chr1:186264684-186264734	HRE	kidney:	n/a
39	chr1:186264674-186264724	T-47D	breast:	n/a
40	chr1:186264684-186264734	PrEC	prostate:	n/a
41	chr1:186264674-186264724	ovcar-3	ovarian:	n/a
42	chr1:186264674-186264724	HL-60	blood:	n/a
43	chr1:186264684-186264734	BJ	skin:	n/a
44	chr1:186264684-186264734	AoSMC	blood vessel:	n/a
45	chr1:186264674-186264724	HCM	heart:	n/a
46	chr1:186264684-186264734	HL-60	blood:	n/a
47	chr1:186264674-186264724	PANC-1	pancreas:	n/a
48	chr1:186264674-186264724	Hepatocyte	liver:	n/a
49	chr1:186264674-186264724	NT2-D1	testis:	n/a
50	chr1:186264674-186264724	HEEpiC	esophagus:	n/a

No data

Variant related genes	Relation type
PRG4	CpG island

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12568251	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12749865	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs33937627	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34926202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55884850	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61831146	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35877985	RNF2	cis	parietal	SCAN
rs35877985	TEDDM1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186259000-186270400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:186259600-186273600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:186259800-186268400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:186260000-186264800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:186260000-186269400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:186260800-186269400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:186261200-186265000	Weak transcription	Hela-S3	cervix
8	chr1:186262400-186268800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:186262600-186264800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:186262600-186264800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:186264600-186265400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:186264600-186265400	Enhancers	Liver	Liver
13	chr1:186264600-186267200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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