Variant report

Variant	rs60664312
Chromosome Location	chr16:75657221-75657222
allele	A/C
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	ATF3	chr16:75657086-75657469	K562	blood:	n/a	chr16:75657190-75657197 chr16:75657189-75657197 chr16:75657190-75657198 chr16:75657186-75657201 chr16:75657187-75657197 chr16:75657189-75657209 chr16:75657188-75657199 chr16:75657188-75657199
2	CHD2	chr16:75656763-75657523	Hela-S3	cervix:	n/a	n/a
3	SP4	chr16:75656868-75657404	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F4	chr16:75656813-75657496	MCF10A-Er-Src	breast:	n/a	chr16:75657289-75657300 chr16:75656973-75656983 chr16:75657190-75657199 chr16:75657188-75657197
5	EGR1	chr16:75656954-75657287	K562	blood:	n/a	chr16:75657238-75657262
6	TAF1	chr16:75656892-75657232	GM12892	blood:	n/a	n/a
7	POLR2A	chr16:75656729-75657547	HL-60	blood:	n/a	n/a
8	BRCA1	chr16:75656782-75657489	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr16:75656563-75657508	H1-neurons	neurons:	n/a	n/a
10	RELA	chr16:75656886-75657443	GM19099	blood:	n/a	n/a
11	ELF1	chr16:75656541-75657567	MCF-7	breast:	n/a	n/a
12	ELF1	chr16:75656510-75657571	MCF-7	breast:	n/a	n/a
13	TEAD4	chr16:75656829-75657436	ECC-1	luminal epithelium:	n/a	n/a
14	SP4	chr16:75656689-75657402	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr16:75654394-75657790	SK-N-SH	brain:	n/a	chr16:75656347-75656356
16	ZBTB33	chr16:75656857-75657700	A549	lung:	n/a	chr16:75656949-75656959
17	ATF2	chr16:75656906-75657534	GM12878	blood:	n/a	chr16:75657188-75657199
18	BCL3	chr16:75656763-75657703	A549	lung:	n/a	chr16:75657216-75657229 chr16:75656788-75656797
19	BRCA1	chr16:75656985-75657478	HepG2	liver:	n/a	n/a
20	TBP	chr16:75656923-75657500	GM12878	blood:	n/a	n/a
21	POLR2A	chr16:75656956-75657400	HCT-116	colon:	n/a	n/a
22	MYC	chr16:75656724-75657428	MCF10A-Er-Src	breast:	n/a	n/a
23	MAX	chr16:75656676-75657564	SK-N-SH	brain:	n/a	n/a
24	MYC	chr16:75656787-75657440	K562	blood:	n/a	n/a
25	ELK4	chr16:75656621-75657449	Hela-S3	cervix:	n/a	n/a
26	MAX	chr16:75656824-75657398	H1-hESC	embryonic stem cell:	n/a	n/a
27	CREB1	chr16:75655962-75657631	GM12878	blood:	n/a	chr16:75657187-75657200
28	MYC	chr16:75656901-75657283	MCF-7	breast:	n/a	n/a
29	EGR1	chr16:75656967-75657269	K562	blood:	n/a	chr16:75657238-75657262
30	CHD2	chr16:75656732-75657612	GM12878	blood:	n/a	n/a
31	TEAD4	chr16:75656904-75657488	K562	blood:	n/a	n/a
32	ETS1	chr16:75656897-75657359	GM12878	blood:	n/a	chr16:75657216-75657229 chr16:75657249-75657262 chr16:75657297-75657310
33	GABPA	chr16:75656955-75657336	GM12878	blood:	n/a	n/a
34	IRF1	chr16:75656454-75657427	K562	blood:	n/a	n/a
35	POLR2A	chr16:75656851-75657359	GM12891	blood:	n/a	n/a
36	NFIC	chr16:75656881-75657504	ECC-1	luminal epithelium:	n/a	n/a
37	TCF12	chr16:75656641-75657595	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr16:75656878-75657464	HepG2	liver:	n/a	n/a
39	POLR2A	chr16:75656937-75657388	A549	lung:	n/a	n/a
40	NR2F2	chr16:75656879-75657560	K562	blood:	n/a	n/a
41	POLR2A	chr16:75656728-75657564	GM12892	blood:	n/a	n/a
42	YY1	chr16:75656741-75657454	HepG2	liver:	n/a	n/a
43	ELF1	chr16:75656613-75657477	K562	blood:	n/a	n/a
44	YY1	chr16:75656993-75657428	SK-N-SH_RA	brain:	n/a	n/a
45	SIX5	chr16:75656646-75657685	A549	lung:	n/a	chr16:75657255-75657264
46	MXI1	chr16:75656681-75657449	HepG2	liver:	n/a	n/a
47	POLR2A	chr16:75656329-75657481	HepG2	liver:	n/a	n/a
48	TAF7	chr16:75656708-75657360	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr16:75656687-75657558	MCF-7	breast:	n/a	n/a
50	MAZ	chr16:75656791-75657457	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:75655020..75658877-chr16:75680481..75684905,8	MCF-7	breast:
2	chr16:75589724..75591808-chr16:75655719..75657999,2	MCF-7	breast:
3	chr16:75653410..75664044-chr16:75674901..75683254,27	MCF-7	breast:
4	chr16:75635717..75638506-chr16:75654475..75657293,3	MCF-7	breast:
5	chr16:810770..811303-chr16:75656696..75657556,2	Hela-S3	cervix:
6	chr16:75467060..75468632-chr16:75654952..75657400,2	K562	blood:
7	chr16:75589928..75591467-chr16:75655261..75657250,2	K562	blood:
8	chr16:75656614..75657376-chr3:149530169..149530933,2	HCT-116	colon:
9	chr16:75656309..75658389-chr16:75681209..75683148,3	K562	blood:
10	chr16:75465910..75469192-chr16:75654368..75658890,6	K562	blood:
11	chr1:46768886..46769886-chr16:75656748..75657385,2	Hela-S3	cervix:
12	chr16:75654016..75659144-chr16:75660095..75666421,8	K562	blood:
13	chr16:75588035..75589877-chr16:75656645..75658476,2	K562	blood:
14	chr16:75587027..75591762-chr16:75651045..75658145,7	K562	blood:
15	chr16:75655386..75658646-chr16:75660355..75663332,4	MCF-7	breast:
16	chr16:75467207..75468752-chr16:75656825..75658775,2	MCF-7	breast:
17	chr16:75656887..75657532-chr9:128508693..128509690,2	MCF-7	breast:

Variant related genes	Relation type
ADAT1	TF binding region
ENSG00000132128	Chromatin interaction
ENSG00000229582	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000205084	Chromatin interaction
ENSG00000167081	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000166848	Chromatin interaction
ENSG00000082996	Chromatin interaction
ENSG00000102854	Chromatin interaction
ENSG00000153774	Chromatin interaction
ENSG00000065457	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10163345	0.85[EUR][1000 genomes]
rs10468346	1.00[ASN][1000 genomes]
rs11546854	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860980	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862453	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864677	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866252	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942022	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942809	0.83[EUR][1000 genomes]
rs16942870	0.83[EUR][1000 genomes]
rs1865492	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1991052	0.83[EUR][1000 genomes]
rs2233803	0.96[EUR][1000 genomes]
rs2233805	0.96[EUR][1000 genomes]
rs2233810	0.96[EUR][1000 genomes]
rs28571860	1.00[ASN][1000 genomes]
rs56892159	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58000098	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58657577	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58996069	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59624897	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59794444	1.00[EUR][1000 genomes]
rs60376290	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60415088	0.94[EUR][1000 genomes]
rs60545422	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61588474	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62619985	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186790	0.94[EUR][1000 genomes]
rs7193257	0.96[EUR][1000 genomes]
rs7195089	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73613267	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73613272	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73615089	0.94[EUR][1000 genomes]
rs8051771	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989360	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60664312	KARS	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75655200-75657600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:75655400-75657600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:75655400-75657800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr16:75655400-75657800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr16:75655600-75657600	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr16:75655800-75657600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:75655800-75657600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:75655800-75657600	Active TSS	GM12878-XiMat	blood
9	chr16:75656000-75657600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr16:75656000-75657800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr16:75656000-75657800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr16:75656000-75657800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr16:75656000-75657800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr16:75656000-75657800	Active TSS	Fetal Brain Female	brain
15	chr16:75656200-75657600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr16:75656200-75657600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr16:75656200-75657600	Active TSS	Aorta	Aorta
18	chr16:75656200-75657600	Active TSS	Fetal Muscle Trunk	muscle
19	chr16:75656200-75657600	Active TSS	Left Ventricle	heart
20	chr16:75656400-75657600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr16:75656400-75657600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr16:75656400-75657600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr16:75656400-75657600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr16:75656400-75657600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr16:75656400-75657600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:75656400-75657600	Active TSS	Colonic Mucosa	Colon
27	chr16:75656400-75657600	Active TSS	Esophagus	oesophagus
28	chr16:75656400-75657600	Active TSS	Fetal Brain Male	brain
29	chr16:75656400-75657600	Active TSS	Fetal Intestine Large	intestine
30	chr16:75656400-75657600	Active TSS	Ovary	ovary
31	chr16:75656400-75657600	Active TSS	Pancreas	Pancrea
32	chr16:75656400-75657600	Active TSS	Placenta Amnion	Placenta Amnion
33	chr16:75656400-75657600	Active TSS	Psoas Muscle	Psoas
34	chr16:75656400-75657800	Active TSS	H1 Cell Line	embryonic stem cell
35	chr16:75656400-75657800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr16:75656400-75657800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr16:75656400-75657800	Active TSS	Brain Germinal Matrix	brain
38	chr16:75656400-75657800	Active TSS	Placenta	Placenta
39	chr16:75656400-75657800	Active TSS	A549	lung
40	chr16:75656400-75658000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr16:75656600-75657400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr16:75656600-75657400	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr16:75656600-75657400	Active TSS	Small Intestine	intestine
44	chr16:75656600-75657400	Active TSS	Hela-S3	cervix
45	chr16:75656600-75657400	Active TSS	HUVEC	blood vessel
46	chr16:75656600-75657600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr16:75656600-75657600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:75656600-75657600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr16:75656600-75657600	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr16:75656600-75657600	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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