Variant report

Variant	rs61631401
Chromosome Location	chr17:19563648-19563649
allele	C/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	HNF4G	chr17:19563573-19564344	HepG2	liver:	n/a	n/a
2	TCF7L2	chr17:19563586-19564075	MCF-7	breast:	n/a	chr17:19563947-19563957 chr17:19563930-19563939 chr17:19563771-19563785 chr17:19563774-19563783
3	MBD4	chr17:19563323-19564444	HepG2	liver:	n/a	n/a
4	CEBPB	chr17:19563569-19564208	HepG2	liver:	n/a	chr17:19563895-19563906 chr17:19563863-19563875
5	TCF7L2	chr17:19563295-19564197	HepG2	liver:	n/a	chr17:19563947-19563957 chr17:19563930-19563939 chr17:19563441-19563448 chr17:19563771-19563785 chr17:19563774-19563783
6	EP300	chr17:19563389-19564246	HepG2	liver:	n/a	chr17:19563816-19563826
7	SMC3	chr17:19563644-19564283	HepG2	liver:	n/a	n/a
8	HNF4G	chr17:19563558-19564387	HepG2	liver:	n/a	chr17:19564367-19564382
9	MAX	chr17:19563441-19564221	HepG2	liver:	n/a	n/a
10	TBP	chr17:19563414-19564239	HepG2	liver:	n/a	n/a
11	EP300	chr17:19563471-19564304	HepG2	liver:	n/a	chr17:19563816-19563826
12	EP300	chr17:19563343-19564416	HepG2	liver:	n/a	chr17:19563816-19563826
13	ARID3A	chr17:19563346-19564460	HepG2	liver:	n/a	n/a
14	FOXA2	chr17:19563452-19564123	A549	lung:	n/a	chr17:19563817-19563829 chr17:19563802-19563814
15	FOXA1	chr17:19563370-19564375	HepG2	liver:	n/a	chr17:19563815-19563830 chr17:19563817-19563829 chr17:19563802-19563814
16	FOXA1	chr17:19563519-19564294	HepG2	liver:	n/a	chr17:19563815-19563830 chr17:19563817-19563829 chr17:19563802-19563814
17	MAX	chr17:19563375-19564439	HepG2	liver:	n/a	n/a
18	POLR2A	chr17:19563323-19564360	HepG2	liver:	n/a	n/a
19	FOXA1	chr17:19563628-19564043	T-47D	breast:	n/a	chr17:19563815-19563830 chr17:19563817-19563829 chr17:19563802-19563814
20	TEAD4	chr17:19563367-19564290	HepG2	liver:	n/a	n/a
21	HDAC2	chr17:19563512-19564343	HepG2	liver:	n/a	chr17:19563817-19563826
22	JUND	chr17:19563563-19564047	HepG2	liver:	n/a	n/a
23	MAFF	chr17:19563613-19564134	HepG2	liver:	n/a	n/a
24	FOXA1	chr17:19563592-19564044	T-47D	breast:	n/a	chr17:19563815-19563830 chr17:19563817-19563829 chr17:19563802-19563814
25	MBD4	chr17:19563493-19564331	HepG2	liver:	n/a	n/a
26	FOXA2	chr17:19563019-19564388	HepG2	liver:	n/a	chr17:19563817-19563829 chr17:19563802-19563814
27	SP1	chr17:19563509-19564369	HepG2	liver:	n/a	chr17:19564311-19564321
28	HEY1	chr17:19563438-19563752	HepG2	liver:	n/a	n/a
29	HNF4A	chr17:19563566-19564366	HepG2	liver:	n/a	n/a
30	TCF12	chr17:19563431-19564217	A549	lung:	n/a	n/a
31	POLR2A	chr17:19563609-19563694	HepG2	liver:	n/a	n/a
32	JUND	chr17:19563387-19564131	HepG2	liver:	n/a	n/a
33	POLR2A	chr17:19562791-19564450	HepG2	liver:	n/a	n/a
34	RXRA	chr17:19563613-19564334	HepG2	liver:	n/a	n/a
35	MYBL2	chr17:19563351-19564399	HepG2	liver:	n/a	n/a
36	MYBL2	chr17:19563450-19564332	HepG2	liver:	n/a	n/a
37	FOXA1	chr17:19563380-19564264	HepG2	liver:	n/a	chr17:19563815-19563830 chr17:19563817-19563829 chr17:19563802-19563814
38	FOXA1	chr17:19563370-19564344	HepG2	liver:	n/a	chr17:19563815-19563830 chr17:19563817-19563829 chr17:19563802-19563814
39	FOXA2	chr17:19563494-19564295	HepG2	liver:	n/a	chr17:19563817-19563829 chr17:19563802-19563814
40	NFIC	chr17:19563469-19564276	HepG2	liver:	n/a	n/a
41	HDAC2	chr17:19563510-19564285	HepG2	liver:	n/a	chr17:19563817-19563826
42	FOSL2	chr17:19563642-19564149	HepG2	liver:	n/a	n/a
43	NFIC	chr17:19563410-19564373	HepG2	liver:	n/a	n/a
44	HNF4A	chr17:19563571-19564261	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19549675..19554690-chr17:19558689..19564889,9	MCF-7	breast:
2	chr17:19558329..19562006-chr17:19563141..19565959,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252349	TF binding region
ALDH3A2	TF binding region
ENSG00000264932	Chromatin interaction
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1004490	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1004491	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1034897	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204407	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12601634	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12604069	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12940877	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12945345	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16960251	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2072332	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2120271	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28672254	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2891951	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35364675	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752046	0.81[EUR][1000 genomes]
rs3786038	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4244600	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621031	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4646793	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646800	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924788	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924791	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925002	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4925026	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925037	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925038	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925040	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4925041	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56262978	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58835440	0.81[EUR][1000 genomes]
rs58970893	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67870359	0.81[EUR][1000 genomes]
rs68066777	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7216938	0.80[EUR][1000 genomes]
rs73981559	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7502080	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962801	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs968012	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9902636	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9909886	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9914765	0.95[AMR][1000 genomes];0.95[EUR][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	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv1062485	chr17:19558644-19608008	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv907865	chr17:19558722-19575721	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61631401	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs61631401	ALDH3A2	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19566800	Weak transcription	Primary B cells from cord blood	blood
2	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:19553400-19566400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:19554800-19574400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr17:19555000-19568800	Weak transcription	NH-A	brain
7	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
9	chr17:19555200-19566400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:19555200-19566600	Weak transcription	NHDF-Ad	bronchial
11	chr17:19555200-19569800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr17:19555200-19576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr17:19555400-19570000	Strong transcription	Fetal Muscle Leg	muscle
14	chr17:19555600-19567200	Weak transcription	Right Atrium	heart
15	chr17:19555600-19569800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
17	chr17:19556200-19569800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr17:19556600-19569800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:19557200-19569800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr17:19558200-19568200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:19558200-19569400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:19558200-19569600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:19558200-19569800	Strong transcription	Fetal Intestine Large	intestine
24	chr17:19558400-19566600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr17:19558400-19566800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:19558400-19567200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr17:19558400-19571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:19558600-19569800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr17:19558800-19566800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr17:19559200-19571800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:19559200-19574200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr17:19559400-19566800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr17:19559400-19575000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr17:19559400-19575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:19559600-19570800	Strong transcription	Brain Anterior Caudate	brain
37	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:19559800-19564800	Weak transcription	Ovary	ovary
39	chr17:19559800-19565200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr17:19559800-19565400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr17:19559800-19577200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr17:19560000-19564600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr17:19560000-19564800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr17:19560000-19564800	Weak transcription	Osteobl	bone
45	chr17:19560000-19565400	Weak transcription	Colon Smooth Muscle	Colon
46	chr17:19560000-19565600	Weak transcription	HSMM	muscle
47	chr17:19560200-19564000	Weak transcription	HSMMtube	muscle
48	chr17:19560200-19565400	Weak transcription	Brain Angular Gyrus	brain
49	chr17:19560200-19565400	Weak transcription	Fetal Kidney	kidney
50	chr17:19560200-19566600	Weak transcription	Fetal Brain Male	brain

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