Variant report

Variant	rs16941008
Chromosome Location	chr16:75656400-75656401
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	POLR2A	chr16:75655886-75656704	GM12892	blood:	n/a	n/a
2	MXI1	chr16:75654394-75657790	SK-N-SH	brain:	n/a	chr16:75656347-75656356
3	POLR2A	chr16:75656295-75656510	ProgFib	skin:	n/a	n/a
4	NFIC	chr16:75655904-75656430	GM12878	blood:	n/a	n/a
5	CREB1	chr16:75655962-75657631	GM12878	blood:	n/a	chr16:75657187-75657200
6	POLR2A	chr16:75656287-75656597	GM12878	blood:	n/a	n/a
7	RCOR1	chr16:75656330-75656530	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:75656253-75656480	K562	blood:	n/a	n/a
9	POLR2A	chr16:75656329-75657481	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:75655900-75656554	GM12892	blood:	n/a	n/a
11	MXI1	chr16:75655976-75657648	IMR90	lung:	n/a	chr16:75656347-75656356
12	REST	chr16:75656265-75657889	H1-neurons	neurons:	n/a	chr16:75656975-75656985
13	POLR2A	chr16:75656333-75657562	K562	blood:	n/a	n/a
14	POLR2A	chr16:75656091-75657482	K562	blood:	n/a	n/a
15	POLR2A	chr16:75656219-75658052	HepG2	liver:	n/a	n/a
16	POLR2A	chr16:75656234-75657530	GM19099	blood:	n/a	n/a
17	BCLAF1	chr16:75655935-75656549	GM12878	blood:	n/a	chr16:75656201-75656210 chr16:75656198-75656207
18	STAT5A	chr16:75655890-75657553	GM12878	blood:	n/a	chr16:75656706-75656713
19	RELA	chr16:75656227-75657447	GM15510	blood:	n/a	n/a
20	POLR2A	chr16:75656324-75657592	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr16:75656085-75657499	K562	blood:	n/a	n/a
22	MTA3	chr16:75655889-75657609	GM12878	blood:	n/a	n/a
23	HCFC1	chr16:75655946-75657800	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr16:75656224-75656461	HUVEC	blood vessel:	n/a	n/a
25	USF2	chr16:75656391-75657516	Hela-S3	cervix:	n/a	n/a
26	ATF2	chr16:75655977-75657594	GM12878	blood:	n/a	chr16:75657188-75657199
27	POLR2A	chr16:75656018-75657543	GM12878	blood:	n/a	n/a
28	MXI1	chr16:75656301-75657415	Hela-S3	cervix:	n/a	chr16:75656347-75656356
29	FOXM1	chr16:75655881-75656550	GM12878	blood:	n/a	n/a
30	PML	chr16:75655890-75657641	GM12878	blood:	n/a	n/a
31	POLR2A	chr16:75655945-75656601	GM12878	blood:	n/a	n/a
32	POLR2A	chr16:75655857-75657606	GM12878	blood:	n/a	n/a
33	POLR2A	chr16:75656245-75657442	Raji	blood:	n/a	n/a
34	POLR2A	chr16:75656249-75657591	MCF10A-Er-Src	breast:	n/a	n/a
35	STAT5A	chr16:75656240-75657303	GM12878	blood:	n/a	chr16:75656706-75656713
36	POLR2A	chr16:75656103-75656702	K562	blood:	n/a	n/a
37	POLR2A	chr16:75656318-75657687	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr16:75656057-75657570	GM12891	blood:	n/a	n/a
39	POLR2A	chr16:75655772-75657585	GM12892	blood:	n/a	n/a
40	POLR2A	chr16:75656307-75656489	MCF-7	breast:	n/a	n/a
41	NFATC1	chr16:75655930-75656628	GM12878	blood:	n/a	n/a
42	POLR2A	chr16:75655692-75657549	GM12892	blood:	n/a	n/a
43	SIN3AK20	chr16:75656289-75657669	MCF-7	breast:	n/a	n/a
44	POLR2A	chr16:75656030-75657614	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr16:75656379-75657905	Hela-S3	cervix:	n/a	n/a
46	SIN3A	chr16:75656244-75657443	H1-hESC	embryonic stem cell:	n/a	n/a
47	MXI1	chr16:75656261-75657397	K562	blood:	n/a	chr16:75656347-75656356
48	FOXM1	chr16:75655957-75657627	GM12878	blood:	n/a	n/a
49	HA-E2F1	chr16:75656261-75657616	MCF-7	breast:	n/a	chr16:75656973-75656983 chr16:75657190-75657199 chr16:75657188-75657197
50	POLR2A	chr16:75656344-75657544	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:75655020..75658877-chr16:75680481..75684905,8	MCF-7	breast:
2	chr16:75496396..75498894-chr16:75652662..75656672,3	MCF-7	breast:
3	chr16:75589724..75591808-chr16:75655719..75657999,2	MCF-7	breast:
4	chr16:75653410..75664044-chr16:75674901..75683254,27	MCF-7	breast:
5	chr16:75635717..75638506-chr16:75654475..75657293,3	MCF-7	breast:
6	chr16:75467060..75468632-chr16:75654952..75657400,2	K562	blood:
7	chr16:75589928..75591467-chr16:75655261..75657250,2	K562	blood:
8	chr16:75656309..75658389-chr16:75681209..75683148,3	K562	blood:
9	chr16:75465910..75469192-chr16:75654368..75658890,6	K562	blood:
10	chr16:75654016..75659144-chr16:75660095..75666421,8	K562	blood:
11	chr16:75598745..75600890-chr16:75655383..75657208,2	MCF-7	breast:
12	chr16:75587027..75591762-chr16:75651045..75658145,7	K562	blood:
13	chr16:75655386..75658646-chr16:75660355..75663332,4	MCF-7	breast:

Variant related genes	Relation type
ADAT1	TF binding region
ENSG00000034713	Chromatin interaction
ENSG00000166822	Chromatin interaction
ENSG00000065457	Chromatin interaction
ENSG00000205084	Chromatin interaction
ENSG00000166848	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000261717	Chromatin interaction
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10163345	0.85[EUR][1000 genomes]
rs10468346	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1133766	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11546854	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11646086	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11646574	1.00[CEU][hapmap]
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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942022	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942809	0.83[EUR][1000 genomes]
rs16942870	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs16943274	1.00[CEU][hapmap]
rs16943285	1.00[CEU][hapmap]
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	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2233810	0.96[EUR][1000 genomes]
rs2242408	0.85[CEU][hapmap]
rs2453141	1.00[JPT][hapmap]
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]
rs60664312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186790	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7193257	0.96[EUR][1000 genomes]
rs7195089	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053257	0.85[CEU][hapmap];1.00[MEX][hapmap]
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
rs16941008	KARS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:157 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75654400-75656400	Weak transcription	Ovary	ovary
2	chr16:75654600-75656400	Enhancers	Primary B cells from peripheral blood	blood
3	chr16:75654600-75656400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr16:75654800-75656400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr16:75654800-75656400	Enhancers	Placenta	Placenta
6	chr16:75655000-75656600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr16:75655200-75656600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr16:75655200-75656600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:75655200-75656600	Flanking Active TSS	HUVEC	blood vessel
10	chr16:75655200-75657600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr16:75655400-75656400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:75655400-75657600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr16:75655400-75657800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr16:75655400-75657800	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr16:75655600-75656400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr16:75655600-75656400	Flanking Active TSS	Fetal Brain Male	brain
17	chr16:75655600-75656400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr16:75655600-75656600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr16:75655600-75656600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr16:75655600-75656600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr16:75655600-75656600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:75655600-75656600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr16:75655600-75656600	Flanking Active TSS	Dnd41	blood
24	chr16:75655600-75656600	Flanking Active TSS	Hela-S3	cervix
25	chr16:75655600-75656600	Flanking Active TSS	NHEK	skin
26	chr16:75655600-75656800	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr16:75655600-75656800	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr16:75655600-75657000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr16:75655600-75657600	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr16:75655800-75656400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr16:75655800-75656400	Enhancers	Stomach Mucosa	stomach
32	chr16:75655800-75656600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr16:75655800-75656600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr16:75655800-75656600	Enhancers	Small Intestine	intestine
35	chr16:75655800-75656600	Enhancers	Spleen	Spleen
36	chr16:75655800-75656600	Flanking Active TSS	HepG2	liver
37	chr16:75655800-75656800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr16:75655800-75656800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr16:75655800-75656800	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr16:75655800-75657600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr16:75655800-75657600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr16:75655800-75657600	Active TSS	GM12878-XiMat	blood
43	chr16:75656000-75656400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr16:75656000-75656400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr16:75656000-75656400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr16:75656000-75656400	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr16:75656000-75656400	Flanking Active TSS	Colonic Mucosa	Colon
48	chr16:75656000-75656400	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr16:75656000-75656400	Enhancers	Lung	lung
50	chr16:75656000-75656400	Enhancers	Right Atrium	heart

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