Variant report

Variant	rs4141177
Chromosome Location	chr17:67099658-67099659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr17:67099192-67100939	K562	blood:	n/a	chr17:67099964-67099973 chr17:67099965-67099982 chr17:67099964-67099971 chr17:67100440-67100450 chr17:67100037-67100047
2	RCOR1	chr17:67099542-67100370	K562	blood:	n/a	n/a
3	STAT5A	chr17:67099575-67100226	K562	blood:	n/a	n/a
4	FOXA1	chr17:67099628-67100191	HepG2	liver:	n/a	n/a
5	ARID3A	chr17:67099561-67100456	K562	blood:	n/a	n/a
6	CHD2	chr17:67099631-67100213	K562	blood:	n/a	n/a
7	BHLHE40	chr17:67099598-67100263	K562	blood:	n/a	n/a
8	MAZ	chr17:67099574-67100249	K562	blood:	n/a	n/a
9	TEAD4	chr17:67099575-67100234	K562	blood:	n/a	n/a
10	JUN	chr17:67099637-67100330	K562	blood:	n/a	n/a
11	ZMIZ1	chr17:67099630-67100266	K562	blood:	n/a	n/a
12	CUX1	chr17:67099618-67100515	K562	blood:	n/a	n/a
13	CBX3	chr17:67099607-67100349	K562	blood:	n/a	n/a
14	MYC	chr17:67099570-67100327	K562	blood:	n/a	n/a
15	NR2F2	chr17:67099565-67100400	K562	blood:	n/a	n/a
16	TBL1XR1	chr17:67099299-67100516	K562	blood:	n/a	n/a
17	GATA1	chr17:67099647-67100310	PBDE	blood:	n/a	chr17:67099964-67099973 chr17:67099965-67099982 chr17:67099964-67099971 chr17:67100037-67100047
18	FOXA2	chr17:67099472-67100359	HepG2	liver:	n/a	n/a
19	MAFK	chr17:67099323-67100266	K562	blood:	n/a	n/a
20	FOXA1	chr17:67099637-67100220	HepG2	liver:	n/a	n/a
21	EP300	chr17:67099455-67100298	K562	blood:	n/a	chr17:67100035-67100049 chr17:67099489-67099503
22	EP300	chr17:67099523-67100554	K562	blood:	n/a	chr17:67100035-67100049 chr17:67100438-67100452 chr17:67100440-67100454 chr17:67100331-67100345
23	JUND	chr17:67099489-67100321	K562	blood:	n/a	n/a
24	TAL1	chr17:67099567-67100400	K562	blood:	n/a	chr17:67099964-67099982
25	CREB1	chr17:67099446-67100272	K562	blood:	n/a	n/a
26	ZNF384	chr17:67099582-67100700	K562	blood:	n/a	n/a
27	UBTF	chr17:67099558-67100322	K562	blood:	n/a	n/a
28	CCNT2	chr17:67099638-67100538	K562	blood:	n/a	chr17:67099962-67099982
29	ATF1	chr17:67099614-67100149	K562	blood:	n/a	n/a
30	ELK1	chr17:67099651-67100039	K562	blood:	n/a	n/a
31	TEAD4	chr17:67099552-67100231	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:67091911..67095488-chr17:67096351..67099862,4	K562	blood:
2	chr17:67088137..67090811-chr17:67098460..67099975,2	K562	blood:
3	chr17:67085517..67087191-chr17:67098879..67100448,2	K562	blood:
4	chr17:67098233..67101602-chr17:67102782..67105641,3	K562	blood:
5	chr17:67099587..67101559-chr17:67104865..67106411,2	K562	blood:
6	chr17:67096035..67097886-chr17:67098176..67100772,2	K562	blood:

Variant related genes	Relation type
ABCA6	TF binding region
ENSG00000154262	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11652530	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11659091	0.81[GIH][hapmap]
rs12162136	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12453914	0.86[CHB][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs12601388	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12939282	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12940298	0.91[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12952117	0.83[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12953127	0.81[CHD][hapmap]
rs16973567	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1990335	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041170	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2041171	0.82[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2190900	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2302134	0.85[JPT][hapmap]
rs3744489	0.84[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4334355	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4603621	0.80[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4968838	0.80[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968839	0.85[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4968843	1.00[ASW][hapmap];0.81[CHD][hapmap]
rs4968849	0.81[CHD][hapmap]
rs4968851	0.81[CHD][hapmap]
rs5025273	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs6501183	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7207609	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7208586	0.83[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7213831	1.00[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7214079	0.90[CEU][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7217887	0.82[ASW][hapmap];0.81[CHD][hapmap]
rs740516	0.82[JPT][hapmap]
rs740520	0.81[CHD][hapmap]
rs7503217	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs763920	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs8064595	0.82[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8074654	0.81[CHD][hapmap]
rs8077252	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8077551	0.81[CHD][hapmap]
rs8078314	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8079981	1.00[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8080863	0.81[CHD][hapmap]
rs9303012	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs976698	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs981452	0.81[CHD][hapmap]
rs9902643	1.00[ASW][hapmap];0.81[CHD][hapmap]
rs9916693	0.87[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs997781	0.83[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[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	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv908705	chr17:67061898-67112456	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	esv1850212	chr17:67081732-67117428	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4141177	CACNG5	cis	cerebellum	SCAN
rs4141177	ABCA6	cis	cerebellum	SCAN
rs4141177	ABCA6	cis	parietal	SCAN
rs4141177	ABCA9	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67067200-67111600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr17:67076800-67109800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr17:67077800-67137800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:67079400-67112200	Strong transcription	Liver	Liver
5	chr17:67079400-67112600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:67079400-67117600	Weak transcription	Esophagus	oesophagus
7	chr17:67079600-67101200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:67079600-67114200	Weak transcription	NHDF-Ad	bronchial
9	chr17:67080800-67112000	Weak transcription	Brain Substantia Nigra	brain
10	chr17:67081200-67102000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr17:67081400-67118600	Weak transcription	Right Ventricle	heart
12	chr17:67082200-67114400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr17:67087000-67114600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr17:67087000-67130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:67089800-67102200	Weak transcription	GM12878-XiMat	blood
16	chr17:67090400-67110000	Strong transcription	Adipose Nuclei	Adipose
17	chr17:67091200-67131400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr17:67091600-67104400	Weak transcription	Left Ventricle	heart
19	chr17:67091600-67130000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr17:67092200-67137600	Weak transcription	Brain Anterior Caudate	brain
21	chr17:67095800-67131000	Weak transcription	Fetal Muscle Leg	muscle
22	chr17:67096200-67143400	Weak transcription	Psoas Muscle	Psoas
23	chr17:67096400-67099800	Weak transcription	Ovary	ovary
24	chr17:67096400-67104400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr17:67096400-67134000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr17:67097000-67133800	Weak transcription	Colon Smooth Muscle	Colon
27	chr17:67097200-67105000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr17:67098600-67103200	Weak transcription	Fetal Lung	lung
29	chr17:67099000-67131600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:67099200-67100600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:67099400-67100200	Flanking Active TSS	K562	blood
32	chr17:67099600-67099800	Active TSS	Pancreas	Pancrea
33	chr17:67099600-67100600	Enhancers	HepG2	liver
34	chr17:67099600-67101200	Enhancers	Gastric	stomach

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