Variant report

Variant	rs2233803
Chromosome Location	chr16:75680795-75680796
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	chr16:75680523-75683108	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr16:75680716-75682035	A549	lung:	n/a	chr16:75681623-75681633
3	POLR2A	chr16:75680761-75682678	HepG2	liver:	n/a	n/a
4	MXI1	chr16:75680338-75684517	SK-N-SH	brain:	n/a	n/a
5	GABPA	chr16:75680648-75682051	MCF-7	breast:	n/a	chr16:75681657-75681671 chr16:75681660-75681674
6	MYC	chr16:75680755-75682715	K562	blood:	n/a	chr16:75681623-75681633
7	POLR2A	chr16:75680668-75683681	PBDE	blood:	n/a	n/a
8	HEY1	chr16:75680474-75681013	K562	blood:	n/a	n/a
9	POLR2A	chr16:75680754-75684242	GM12891	blood:	n/a	n/a
10	MXI1	chr16:75680549-75684242	IMR90	lung:	n/a	n/a
11	HCFC1	chr16:75680408-75682898	Hela-S3	cervix:	n/a	n/a
12	IRF1	chr16:75680783-75682720	K562	blood:	n/a	chr16:75681174-75681186 chr16:75681173-75681186 chr16:75681171-75681188 chr16:75681624-75681638 chr16:75681174-75681185 chr16:75681174-75681188 chr16:75681173-75681193 chr16:75681172-75681186 chr16:75681174-75681187 chr16:75682554-75682568 chr16:75681173-75681187 chr16:75681175-75681189 chr16:75681174-75681187 chr16:75681174-75681186
13	POLR2A	chr16:75680684-75681947	K562	blood:	n/a	n/a
14	POLR2A	chr16:75680781-75682770	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:75466586..75469509-chr16:75679295..75683235,4	K562	blood:
2	chr16:75466173..75469509-chr16:75680461..75683235,3	K562	blood:
3	chr16:75495991..75500241-chr16:75679416..75683319,6	MCF-7	breast:
4	chr16:75548080..75552218-chr16:75679936..75683385,4	K562	blood:
5	chr16:75680135..75682966-chr16:77223241..77226200,3	MCF-7	breast:
6	chr16:75680522..75683233-chr16:77224728..77226496,3	MCF-7	breast:
7	chr16:75655020..75658877-chr16:75680481..75684905,8	MCF-7	breast:
8	chr16:75634260..75637164-chr16:75680044..75681999,3	K562	blood:
9	chr16:75653410..75664044-chr16:75674901..75683254,27	MCF-7	breast:

Variant related genes	Relation type
TERF2IP	TF binding region
ENSG00000065427	Chromatin interaction
ENSG00000153774	Chromatin interaction
ENSG00000166822	Chromatin interaction
ENSG00000103111	Chromatin interaction
ENSG00000065457	Chromatin interaction
ENSG00000262583	Chromatin interaction
ENSG00000261717	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10163345	0.85[EUR][1000 genomes]
rs1133766	0.82[EUR][1000 genomes]
rs11546854	0.96[EUR][1000 genomes]
rs11640406	0.82[EUR][1000 genomes]
rs11640743	0.82[EUR][1000 genomes]
rs11641108	0.82[EUR][1000 genomes]
rs11646086	0.82[EUR][1000 genomes]
rs11646574	0.82[EUR][1000 genomes]
rs11648206	0.82[EUR][1000 genomes]
rs11649504	0.82[EUR][1000 genomes]
rs11649505	0.82[EUR][1000 genomes]
rs11649571	0.82[EUR][1000 genomes]
rs11860980	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11862453	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11864677	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11866252	0.96[EUR][1000 genomes]
rs16941008	0.96[EUR][1000 genomes]
rs16942022	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16942809	0.87[EUR][1000 genomes]
rs16942870	0.87[EUR][1000 genomes]
rs1865492	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991052	0.87[EUR][1000 genomes]
rs2233805	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233810	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35135836	0.82[EUR][1000 genomes]
rs56892159	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58000098	0.96[EUR][1000 genomes]
rs58657577	0.96[EUR][1000 genomes]
rs58996069	0.96[EUR][1000 genomes]
rs59624897	0.96[EUR][1000 genomes]
rs59794444	0.96[EUR][1000 genomes]
rs60376290	1.00[EUR][1000 genomes]
rs60415088	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60545422	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60664312	0.96[EUR][1000 genomes]
rs61588474	0.96[EUR][1000 genomes]
rs62619985	0.96[EUR][1000 genomes]
rs6834	0.93[EUR][1000 genomes]
rs7186790	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7195089	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73613267	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73613272	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73615089	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051771	0.96[EUR][1000 genomes]
rs9989360	0.98[EUR][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
rs2233803	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	chr16:75679400-75680800	Flanking Active TSS	GM12878-XiMat	blood
2	chr16:75679600-75680800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr16:75679600-75681000	Enhancers	Spleen	Spleen
4	chr16:75679600-75681000	Flanking Active TSS	Hela-S3	cervix
5	chr16:75679800-75681000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr16:75679800-75684600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr16:75680000-75680800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr16:75680000-75680800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr16:75680000-75680800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr16:75680000-75680800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr16:75680000-75681000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr16:75680000-75681000	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr16:75680000-75681200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr16:75680000-75683800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr16:75680000-75683800	Active TSS	A549	lung
16	chr16:75680000-75684400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr16:75680000-75684800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr16:75680200-75680800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr16:75680200-75680800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr16:75680200-75680800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr16:75680200-75680800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr16:75680200-75680800	Enhancers	Placenta	Placenta
23	chr16:75680200-75680800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr16:75680200-75680800	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr16:75680200-75681000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr16:75680200-75681000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr16:75680200-75681000	Flanking Active TSS	Liver	Liver
28	chr16:75680200-75681000	Flanking Active TSS	Fetal Brain Female	brain
29	chr16:75680200-75681200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr16:75680200-75683800	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr16:75680200-75684000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr16:75680200-75684600	Active TSS	K562	blood
33	chr16:75680200-75684800	Active TSS	HSMM	muscle
34	chr16:75680200-75685400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr16:75680200-75685400	Active TSS	NHLF	lung
36	chr16:75680400-75680800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr16:75680400-75680800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr16:75680400-75680800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
39	chr16:75680400-75680800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr16:75680400-75680800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr16:75680400-75680800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr16:75680400-75680800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr16:75680400-75680800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr16:75680400-75680800	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr16:75680400-75680800	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr16:75680400-75680800	Flanking Active TSS	Fetal Muscle Trunk	muscle
47	chr16:75680400-75680800	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr16:75680400-75680800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
49	chr16:75680400-75680800	Flanking Active TSS	Fetal Thymus	thymus
50	chr16:75680400-75680800	Flanking Active TSS	Ovary	ovary

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