Variant report

Variant	rs555754
Chromosome Location	chr6:160769423-160769424
allele	C/T
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	MYC	chr6:160768564-160769797	A549	lung:	n/a	chr6:160769288-160769298
2	FOXA1	chr6:160769072-160769567	HepG2	liver:	n/a	n/a
3	TAF1	chr6:160769008-160770246	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:160768952-160770553	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:160769237-160769613	HepG2	liver:	n/a	n/a
6	MAX	chr6:160768432-160770495	H1-hESC	embryonic stem cell:	n/a	chr6:160769288-160769298 chr6:160768434-160768443
7	POLR2A	chr6:160769279-160770403	Hela-S3	cervix:	n/a	n/a
8	CREB1	chr6:160768711-160769598	A549	lung:	n/a	n/a
9	HDAC2	chr6:160769056-160769586	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:160768766-160770345	Hela-S3	cervix:	n/a	n/a
11	TCF7L2	chr6:160768977-160770500	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:160768540-160770384	HepG2	liver:	n/a	n/a
13	MXI1	chr6:160769378-160770593	HepG2	liver:	n/a	n/a
14	POLR2A	chr6:160769308-160769631	HepG2	liver:	n/a	n/a
15	MAX	chr6:160768510-160770812	HepG2	liver:	n/a	chr6:160770613-160770623 chr6:160769288-160769298
16	POLR2A	chr6:160768551-160770400	A549	lung:	n/a	n/a
17	MAX	chr6:160769373-160769599	A549	lung:	n/a	n/a
18	MAZ	chr6:160769028-160769616	HepG2	liver:	n/a	chr6:160769288-160769298
19	MAX	chr6:160769313-160770413	HepG2	liver:	n/a	n/a
20	MAX	chr6:160768373-160770407	H1-hESC	embryonic stem cell:	n/a	chr6:160769288-160769298 chr6:160768434-160768443
21	TBP	chr6:160769324-160769548	HepG2	liver:	n/a	n/a
22	MAZ	chr6:160768763-160770026	Hela-S3	cervix:	n/a	chr6:160769288-160769298
23	POLR2A	chr6:160769256-160770511	HepG2	liver:	n/a	n/a
24	MAX	chr6:160768714-160770475	Hela-S3	cervix:	n/a	chr6:160769288-160769298
25	YY1	chr6:160768632-160770408	HepG2	liver:	n/a	chr6:160769316-160769330 chr6:160769296-160769305 chr6:160769294-160769305
26	CEBPD	chr6:160769058-160769495	HepG2	liver:	n/a	n/a
27	HEY1	chr6:160768762-160769594	HepG2	liver:	n/a	chr6:160769291-160769306 chr6:160769181-160769196 chr6:160769110-160769125
28	POLR2A	chr6:160768739-160770315	A549	lung:	n/a	n/a
29	POLR2A	chr6:160769070-160770087	A549	lung:	n/a	n/a
30	TAF1	chr6:160769369-160769755	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr6:160768462-160770528	A549	lung:	n/a	chr6:160769288-160769298
32	TAF1	chr6:160769259-160769970	A549	lung:	n/a	n/a
33	MAX	chr6:160768539-160770515	HepG2	liver:	n/a	chr6:160769288-160769298
34	E2F6	chr6:160768274-160770577	H1-hESC	embryonic stem cell:	n/a	chr6:160769906-160769918 chr6:160768500-160768512
35	TAF1	chr6:160768667-160770418	HepG2	liver:	n/a	n/a
36	MAX	chr6:160768323-160771389	A549	lung:	n/a	chr6:160770613-160770623 chr6:160769288-160769298 chr6:160768434-160768443
37	SMARCB1	chr6:160768336-160770306	Hela-S3	cervix:	n/a	n/a
38	E2F6	chr6:160769340-160769649	A549	lung:	n/a	n/a
39	POLR2A	chr6:160769320-160769582	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:160768690-160770056	A549	lung:	n/a	n/a
41	E2F6	chr6:160769257-160769674	A549	lung:	n/a	n/a
42	RCOR1	chr6:160769409-160769622	HepG2	liver:	n/a	n/a
43	CTBP2	chr6:160768280-160770234	H1-hESC	embryonic stem cell:	n/a	n/a
44	GABPA	chr6:160768814-160769869	H1-hESC	embryonic stem cell:	n/a	n/a
45	E2F6	chr6:160769207-160770485	H1-hESC	embryonic stem cell:	n/a	chr6:160769906-160769918
46	CHD2	chr6:160768773-160770364	Hela-S3	cervix:	n/a	chr6:160769361-160769371
47	POLR2A	chr6:160769032-160770080	A549	lung:	n/a	n/a
48	RAD21	chr6:160769238-160769686	HepG2	liver:	n/a	n/a
49	HEY1	chr6:160769234-160770447	HepG2	liver:	n/a	chr6:160769291-160769306

Variant related genes	Relation type
SLC22A3	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10945670	0.84[EUR][1000 genomes]
rs1317652	0.84[EUR][1000 genomes]
rs1605963	0.84[EUR][1000 genomes]
rs1605964	0.84[EUR][1000 genomes]
rs1605965	0.87[ASN][1000 genomes]
rs2136676	0.84[EUR][1000 genomes]
rs2313453	0.84[EUR][1000 genomes]
rs2661845	0.80[ASN][1000 genomes]
rs2665357	0.80[EUR][1000 genomes]
rs2872317	0.84[EUR][1000 genomes]
rs3105748	0.84[EUR][1000 genomes]
rs3105749	0.84[EUR][1000 genomes]
rs3105752	0.84[EUR][1000 genomes]
rs3123633	0.85[EUR][1000 genomes]
rs3123634	0.85[EUR][1000 genomes]
rs3127574	0.85[EUR][1000 genomes]
rs316172	0.87[ASN][1000 genomes]
rs316177	0.87[ASN][1000 genomes]
rs366608	0.88[ASN][1000 genomes]
rs367213	0.87[ASN][1000 genomes]
rs372665	0.87[ASN][1000 genomes]
rs377551	0.92[ASN][1000 genomes]
rs383420	0.87[ASN][1000 genomes]
rs394487	0.92[ASN][1000 genomes]
rs396843	0.87[ASN][1000 genomes]
rs401746	0.87[ASN][1000 genomes]
rs405405	0.92[ASN][1000 genomes]
rs416879	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4235926	0.85[EUR][1000 genomes]
rs423961	0.87[ASN][1000 genomes]
rs425983	0.87[ASN][1000 genomes]
rs431747	0.88[ASN][1000 genomes]
rs435421	0.88[ASN][1000 genomes]
rs445849	0.88[ASN][1000 genomes]
rs4709425	0.85[EUR][1000 genomes]
rs4709426	0.84[EUR][1000 genomes]
rs474513	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs486339	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486359	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487060	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487152	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490275	0.88[ASN][1000 genomes]
rs501470	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs505870	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs506823	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs509707	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518295	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs519118	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs520685	0.91[ASN][1000 genomes]
rs520829	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs537937	0.88[ASN][1000 genomes]
rs539298	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539958	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs541091	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs543159	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs547290	0.87[ASN][1000 genomes]
rs569919	0.87[ASN][1000 genomes]
rs575719	0.83[ASN][1000 genomes]
rs575796	0.87[ASN][1000 genomes]
rs581556	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609562	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622217	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624319	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs634916	0.87[ASN][1000 genomes]
rs637614	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs639426	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641990	0.90[EUR][1000 genomes]
rs668871	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs673259	0.91[ASN][1000 genomes]
rs673736	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs675162	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6905958	0.85[EUR][1000 genomes]
rs6923921	0.85[EUR][1000 genomes]
rs695174	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs884742	0.84[EUR][1000 genomes]
rs9346816	0.89[EUR][1000 genomes]
rs9364552	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1030746	chr6:160592321-160867031	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538493	chr6:160592321-160867031	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030171	chr6:160648469-161091864	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv886809	chr6:160670494-160979275	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv886810	chr6:160700769-160897872	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv886811	chr6:160700769-161070990	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv886812	chr6:160706661-161024848	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	esv3446643	chr6:160767862-160771710	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
14	esv3424011	chr6:160768387-160770935	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160768200-160770200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:160768400-160770000	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr6:160768400-160770600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:160768600-160769600	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:160768600-160769800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:160768600-160770000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:160768600-160770600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr6:160768600-160770800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:160768600-160771000	Bivalent/Poised TSS	HepG2	liver
10	chr6:160768600-160771400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:160768600-160771600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:160768800-160769600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:160768800-160769600	Active TSS	Stomach Smooth Muscle	stomach
14	chr6:160768800-160769800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:160768800-160769800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:160768800-160769800	Active TSS	Liver	Liver
17	chr6:160768800-160769800	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr6:160768800-160769800	Bivalent Enhancer	Spleen	Spleen
19	chr6:160768800-160770000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:160768800-160770000	Active TSS	Hela-S3	cervix
21	chr6:160768800-160770200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:160768800-160770400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:160768800-160770400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:160768800-160771000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:160768800-160771200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:160768800-160771600	Active TSS	A549	lung
27	chr6:160768800-160771800	Active TSS	Aorta	Aorta
28	chr6:160769000-160769600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:160769000-160769600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:160769000-160769800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:160769000-160769800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:160769000-160769800	Active TSS	Adipose Nuclei	Adipose
33	chr6:160769000-160769800	Active TSS	Esophagus	oesophagus
34	chr6:160769000-160769800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr6:160769000-160769800	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr6:160769000-160769800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
37	chr6:160769000-160769800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
38	chr6:160769000-160769800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
39	chr6:160769000-160769800	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr6:160769000-160769800	Active TSS	NH-A	brain
41	chr6:160769000-160770000	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:160769000-160770200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
43	chr6:160769000-160770200	Active TSS	Left Ventricle	heart
44	chr6:160769000-160770400	Active TSS	Right Ventricle	heart
45	chr6:160769000-160770600	Active TSS	Ovary	ovary
46	chr6:160769000-160771000	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr6:160769000-160771000	Active TSS	Rectal Smooth Muscle	rectum
48	chr6:160769000-160771400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:160769000-160771400	Active TSS	Right Atrium	heart
50	chr6:160769000-160772000	Active TSS	Psoas Muscle	Psoas

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