Variant report

Variant	rs3797774
Chromosome Location	chr5:179193970-179193971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr5:179193345-179194320	PBDE	blood:	n/a	chr5:179194046-179194063
2	POLR2A	chr5:179191688-179193979	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:179193094..179194973-chr5:179497469..179499850,2	K562	blood:
2	chr5:179192837..179195567-chr5:179212671..179216209,3	K562	blood:
3	chr5:179191220..179194008-chr5:179228937..179231114,2	K562	blood:
4	chr1:149223887..149224483-chr5:179193253..179194234,3	MCF-7	breast:
5	chr5:179192355..179194197-chr5:179212856..179215229,2	MCF-7	breast:
6	chr5:179192926..179195030-chr5:179200613..179202484,2	MCF-7	breast:
7	chr5:179159859..179161740-chr5:179192124..179194566,2	MCF-7	breast:
8	chr5:179189180..179191928-chr5:179192012..179195048,3	K562	blood:
9	chr5:179183781..179185717-chr5:179193398..179195095,2	K562	blood:
10	chr5:179190740..179195492-chr5:179198923..179204539,8	MCF-7	breast:
11	chr5:179192430..179194832-chr5:179221034..179223075,2	MCF-7	breast:
12	chr5:179190822..179197512-chr5:179244986..179249382,7	K562	blood:
13	chr5:179192485..179195191-chr5:179221488..179224022,4	MCF-7	breast:
14	chr5:179192680..179196164-chr5:179217971..179221244,3	MCF-7	breast:
15	chr5:179186999..179190414-chr5:179192166..179194492,3	MCF-7	breast:

No data

Variant related genes	Relation type
MAML1	TF binding region
ENSG00000161011	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1019443	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10447303	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10447304	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10516146	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10794700	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10903245	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11744662	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12374446	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12374485	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12522926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12652934	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs13172893	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13174472	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13182141	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs13184690	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34329357	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34646062	0.85[CEU][hapmap]
rs34785307	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35320050	0.87[EUR][1000 genomes]
rs56227602	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56807514	0.85[EUR][1000 genomes]
rs62404348	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62406180	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601073	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7736300	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS 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 miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3797774	CANX	cis	parietal	SCAN
rs3797774	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs3797774	C5orf45	cis	cerebellum	SCAN
rs3797774	CANX	cis	cerebellum	SCAN
rs3797774	MAML1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179189800-179194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:179190600-179194800	Enhancers	Right Atrium	heart
3	chr5:179190800-179207600	Strong transcription	Dnd41	blood
4	chr5:179191000-179203000	Weak transcription	Psoas Muscle	Psoas
5	chr5:179191200-179195400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:179191200-179196000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:179191200-179210400	Strong transcription	Thymus	Thymus
8	chr5:179192000-179194000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:179192000-179194000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:179192000-179194400	Genic enhancers	Stomach Smooth Muscle	stomach
11	chr5:179192000-179200000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr5:179192000-179202000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:179192000-179207800	Strong transcription	Fetal Thymus	thymus
14	chr5:179192200-179194000	Genic enhancers	Brain Substantia Nigra	brain
15	chr5:179192200-179194000	Strong transcription	Colonic Mucosa	Colon
16	chr5:179192200-179194400	Genic enhancers	A549	lung
17	chr5:179192200-179194600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:179192200-179194800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:179192200-179194800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:179192200-179194800	Strong transcription	Fetal Kidney	kidney
21	chr5:179192200-179195600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:179192200-179200000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
23	chr5:179192200-179206200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:179192200-179206200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr5:179192200-179206400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:179192200-179206400	Strong transcription	HepG2	liver
27	chr5:179192200-179207600	Strong transcription	Fetal Lung	lung
28	chr5:179192200-179207800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr5:179192200-179208000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:179192200-179210400	Strong transcription	Brain Germinal Matrix	brain
31	chr5:179192400-179194000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
32	chr5:179192400-179194200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:179192400-179194200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:179192400-179194200	Genic enhancers	Brain Anterior Caudate	brain
35	chr5:179192400-179194800	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr5:179192400-179194800	Genic enhancers	Adipose Nuclei	Adipose
37	chr5:179192400-179194800	Genic enhancers	Duodenum Mucosa	Duodenum
38	chr5:179192400-179203600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr5:179192400-179205400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:179192400-179206200	Strong transcription	GM12878-XiMat	blood
41	chr5:179192400-179207600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:179192400-179207600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr5:179192600-179194000	Genic enhancers	Brain Angular Gyrus	brain
44	chr5:179192600-179194000	Genic enhancers	Colon Smooth Muscle	Colon
45	chr5:179192600-179194000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr5:179192600-179194000	Genic enhancers	NHDF-Ad	bronchial
47	chr5:179192600-179194200	Genic enhancers	Primary monocytes fromperipheralblood	blood
48	chr5:179192600-179196800	Strong transcription	Gastric	stomach
49	chr5:179192600-179209800	Strong transcription	Primary T cells from cord blood	blood
50	chr5:179192800-179194400	Genic enhancers	Right Ventricle	heart

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