Variant report

Variant	rs3806596
Chromosome Location	chr2:234637707-234637708
allele	A/G
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:1)
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	chr2:234637667-234637717	CMK	blood:	n/a
2	chr2:234637667-234637717	MCF-7	breast:	n/a
3	chr2:234637667-234637717	HIPEpiC	eye:	n/a
4	chr2:234637667-234637717	ovcar-3	ovarian:	n/a
5	chr2:234637667-234637717	GM12892	blood:	n/a
6	chr2:234637667-234637717	AG04449	skin:	fetal
7	chr2:234637667-234637717	HRE	kidney:	n/a
8	chr2:234637667-234637717	HAEpiC	amniotic membrane:	n/a
9	chr2:234637667-234637717	AoSMC	blood vessel:	n/a
10	chr2:234637667-234637717	RPTEC	kidney:	n/a
11	chr2:234637667-234637717	K562	blood:	n/a
12	chr2:234637667-234637717	SK-N-MC	brain:	n/a
13	chr2:234637667-234637717	HCF	heart:	n/a
14	chr2:234637667-234637717	HEEpiC	esophagus:	n/a
15	chr2:234637667-234637717	ProgFib	skin:	n/a
16	chr2:234637667-234637717	A549	lung:	n/a
17	chr2:234637667-234637717	SK-N-SH_RA	brain:	n/a
18	chr2:234637667-234637717	Jurkat	blood:	n/a
19	chr2:234637667-234637717	HRCEpiC	kidney:	n/a
20	chr2:234637667-234637717	H1-hESC	embryonic stem cell:	embryo
21	chr2:234637667-234637717	HMEC	breast:	n/a
22	chr2:234637667-234637717	NHDF-neo	bronchial:	n/a
23	chr2:234637667-234637717	HEK293	kidney:	embryo
24	chr2:234637667-234637717	GM06990	blood:	n/a
25	chr2:234637667-234637717	HCT-116	colon:	n/a
26	chr2:234637667-234637717	LNCaP	prostate:	n/a
27	chr2:234637667-234637717	AG09309	skin:	n/a
28	chr2:234637667-234637717	HUVEC	blood vessel:	n/a
29	chr2:234637667-234637717	NH-A	brain:	n/a
30	chr2:234637667-234637717	PANC-1	pancreas:	n/a
31	chr2:234637667-234637717	GM12891	blood:	n/a
32	chr2:234637667-234637717	IMR90	lung:	fetal
33	chr2:234637667-234637717	PrEC	prostate:	n/a
34	chr2:234637667-234637717	BE2_C	brain:	n/a
35	chr2:234637667-234637717	MCF10A-Er-Src	breast:	n/a
36	chr2:234637667-234637717	GM12878	blood:	n/a
37	chr2:234637667-234637717	HPAEpiC	pulmonary alveolar:	n/a
38	chr2:234637667-234637717	Hela-S3	cervix:	n/a
39	chr2:234637667-234637717	SKMC	muscle:	n/a
40	chr2:234637667-234637717	SAEC	small airway:	n/a
41	chr2:234637667-234637717	NHBE	bronchial:	n/a
42	chr2:234637667-234637717	HRPEpiC	eye:	n/a
43	chr2:234637667-234637717	PFSK-1	brain:	n/a
44	chr2:234637667-234637717	ECC-1	luminal epithelium:	n/a
45	chr2:234637667-234637717	HNPCEpiC	eye:	n/a
46	chr2:234637667-234637717	Caco-2	colon:	n/a
47	chr2:234637667-234637717	GM19239	blood:	n/a
48	chr2:234637667-234637717	HCPEpiC	choroid plexus:	n/a
49	chr2:234637667-234637717	NB4	blood:	n/a
50	chr2:234637667-234637717	U87	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	2:234635414-234639782..2:234772667-234780240	Hela-S3	cervix:

No data

Variant related genes	Relation type
UGT1A3	CpG island
UGT1A8	CpG island
ENSG00000224287	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10179091	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10929301	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1104892	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11685892	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17862866	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2008595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2012734	0.82[ASN][1000 genomes]
rs2221198	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2363116	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755319	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs3821242	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4124874	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4148326	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233633	0.81[CHB][hapmap]
rs4294999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4399719	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4467260	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4521035	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4663325	0.81[CHB][hapmap]
rs4663327	0.81[CHB][hapmap]
rs4663333	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4663963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4663965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4663967	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4663969	0.92[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4663971	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6431628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6706232	0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711351	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715325	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741669	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6760025	1.00[YRI][hapmap]
rs7556676	0.92[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7572563	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7574296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759174	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7597496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs871514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv2760615	chr2:234613030-234640233	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv3429693	chr2:234627837-234638254	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv3215	chr2:234631123-234670276	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer 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	esv1811811	chr2:234633964-234709430	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv963782	chr2:234636877-234638804	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3806596	DGKD	cis	cerebellum	SCAN
rs3806596	SH3BP4	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234620400-234659200	Weak transcription	Colonic Mucosa	Colon
2	chr2:234620600-234652200	Weak transcription	Esophagus	oesophagus
3	chr2:234626200-234649600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:234626600-234668400	Weak transcription	NHEK	skin
5	chr2:234634600-234639400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:234634600-234648400	Weak transcription	A549	lung
7	chr2:234636000-234639000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:234636200-234638400	Enhancers	Fetal Intestine Small	intestine
9	chr2:234637000-234638200	Enhancers	Stomach Mucosa	stomach
10	chr2:234637200-234638000	Enhancers	Gastric	stomach
11	chr2:234637400-234637800	Enhancers	Liver	Liver
12	chr2:234637600-234638200	Bivalent Enhancer	HepG2	liver

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