Variant report

Variant	rs3804416
Chromosome Location	chr4:102177010-102177011
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:102176705..102178742-chr4:102180562..102183503,2	MCF-7	breast:
2	chr4:102176549..102177185-chr7:130584950..130585525,2	HCT-116	colon:
3	chr4:102171123..102173007-chr4:102176069..102177893,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10004357	0.95[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10009468	0.88[EUR][1000 genomes]
rs10009785	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10016548	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10016669	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10050344	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10516470	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11933861	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11934140	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11937437	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11941610	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11941991	0.91[EUR][1000 genomes]
rs11944013	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11946537	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13103487	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13112866	0.80[CHB][hapmap]
rs13115148	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13115754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13116679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13117915	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13117949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13123962	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13137393	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13151505	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1561721	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1837773	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2048072	0.80[JPT][hapmap]
rs2135611	0.85[CHB][hapmap]
rs2165505	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2583384	0.94[EUR][1000 genomes]
rs2583398	0.83[ASW][hapmap]
rs2583399	0.83[ASW][hapmap]
rs2583405	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2583407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28411074	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28478920	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850335	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850338	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850350	0.82[JPT][hapmap]
rs2850355	0.81[JPT][hapmap]
rs2850359	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850960	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850961	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850971	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28513937	0.88[EUR][1000 genomes]
rs28638776	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28698954	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35095772	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3789748	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3804381	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804382	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804390	0.92[EUR][1000 genomes]
rs3804393	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804403	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs3804404	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3804406	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804407	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804408	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804409	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804410	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804417	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804420	0.91[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804421	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811063	0.86[CHB][hapmap]
rs3827771	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3827773	0.95[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs4413408	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4461528	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4525978	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4699139	0.94[EUR][1000 genomes]
rs4699144	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699163	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60154086	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6532922	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6854591	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6854624	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs713454	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs713455	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs750032	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs925028	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs958379	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs962385	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs962386	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs978373	0.86[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9997767	0.95[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3804416	CXXC4	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102157800-102179600	Weak transcription	Primary B cells from cord blood	blood
2	chr4:102159200-102179800	Weak transcription	Psoas Muscle	Psoas
3	chr4:102161000-102177400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr4:102161000-102177400	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:102166200-102177400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:102166200-102179400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:102173200-102179400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:102173400-102177200	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:102174000-102181200	Weak transcription	Brain Anterior Caudate	brain
10	chr4:102174200-102177200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:102174200-102177400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:102174200-102177400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:102174200-102177600	Weak transcription	Small Intestine	intestine
14	chr4:102174200-102178800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:102174200-102179400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:102174200-102179600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:102174200-102179800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:102174200-102180000	Weak transcription	Left Ventricle	heart
19	chr4:102174200-102181000	Weak transcription	Adipose Nuclei	Adipose
20	chr4:102174200-102186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:102174400-102177400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:102174400-102177400	Weak transcription	HepG2	liver
23	chr4:102174400-102180000	Weak transcription	NHDF-Ad	bronchial
24	chr4:102174400-102180600	Weak transcription	NHLF	lung
25	chr4:102174400-102185800	Weak transcription	HMEC	breast
26	chr4:102174600-102177200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:102174600-102177200	Weak transcription	A549	lung
28	chr4:102174600-102179800	Weak transcription	Ovary	ovary
29	chr4:102175000-102177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr4:102175200-102180000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:102175400-102179800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr4:102175800-102179000	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr4:102175800-102180400	Weak transcription	NH-A	brain
34	chr4:102176000-102177400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:102176000-102177800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr4:102176000-102178000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr4:102176000-102178200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr4:102176000-102178200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr4:102176000-102179600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr4:102176200-102181000	Weak transcription	Fetal Kidney	kidney
41	chr4:102176400-102180400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:102176600-102178200	Enhancers	HUVEC	blood vessel
43	chr4:102176600-102179800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:102176800-102178000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr4:102177000-102177200	Enhancers	Stomach Mucosa	stomach
46	chr4:102177000-102177800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:102177000-102178200	Enhancers	HUES48 Cell Line	embryonic stem cell

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