Variant report

Variant	rs16941301
Chromosome Location	chr16:75665494-75665495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75664761-75667001	GM12892	blood:	n/a	n/a
2	POLR2A	chr16:75664883-75667294	K562	blood:	n/a	n/a
3	POLR2A	chr16:75664960-75665911	GM12891	blood:	n/a	n/a
4	POLR2A	chr16:75665217-75665821	K562	blood:	n/a	n/a
5	POLR2A	chr16:75665239-75665800	K562	blood:	n/a	n/a
6	POLR2A	chr16:75665137-75665840	GM12892	blood:	n/a	n/a
7	POLR2A	chr16:75665468-75665844	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:75665425-75665809	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr16:75665383-75665992	K562	blood:	n/a	n/a
10	CHD2	chr16:75665421-75665746	K562	blood:	n/a	n/a
11	POLR2A	chr16:75665431-75665922	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr16:75665328-75665565	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr16:75665255-75666890	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:75665218-75665839	K562	blood:	n/a	n/a
15	POLR2A	chr16:75665482-75665822	HepG2	liver:	n/a	n/a
16	POLR2A	chr16:75665305-75665556	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr16:75665425-75665632	GM12878	blood:	n/a	n/a
18	POLR2A	chr16:75665082-75665846	GM12892	blood:	n/a	n/a
19	POLR2A	chr16:75664991-75665716	HepG2	liver:	n/a	n/a
20	POLR2A	chr16:75664816-75667313	GM12878	blood:	n/a	n/a
21	POLR2A	chr16:75665185-75665873	GM12891	blood:	n/a	n/a
22	POLR2A	chr16:75665371-75665774	MCF-7	breast:	n/a	n/a
23	POLR2A	chr16:75665155-75665858	GM12892	blood:	n/a	n/a
24	POLR2A	chr16:75665239-75665846	K562	blood:	n/a	n/a
25	POLR2A	chr16:75665207-75665833	GM12891	blood:	n/a	n/a
26	POLR2A	chr16:75665275-75665832	GM12878	blood:	n/a	n/a
27	POLR2A	chr16:75665033-75665794	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr16:75665147-75665837	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr16:75665153-75665789	A549	lung:	n/a	n/a
30	POLR2A	chr16:75665340-75665751	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75665324..75667854-chr16:75669001..75671047,2	MCF-7	breast:
2	chr16:75659107..75663905-chr16:75664441..75666503,5	MCF-7	breast:
3	chr16:75654016..75659144-chr16:75660095..75666421,8	K562	blood:

No data

Variant related genes	Relation type
KARS	TF binding region
ENSG00000065427	Chromatin interaction
ENSG00000065457	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11556641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12922861	1.00[CEU][hapmap]
rs16940260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16940348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16940362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16940444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16941287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975847	1.00[CHB][hapmap]
rs2164246	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2550320	1.00[AMR][1000 genomes]
rs2550889	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2550892	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2550893	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2550897	1.00[AMR][1000 genomes]
rs2550900	1.00[AMR][1000 genomes]
rs2550902	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2550903	1.00[AMR][1000 genomes]
rs2550906	1.00[AMR][1000 genomes]
rs2550914	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2550915	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2641803	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2641807	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650410	1.00[AMR][1000 genomes]
rs2650411	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs2650413	0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2738800	1.00[AMR][1000 genomes]
rs55714466	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55862257	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56030666	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321575	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60919196	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7194333	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72563121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74024796	1.00[AMR][1000 genomes]
rs74027409	1.00[AMR][1000 genomes]
rs74027420	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027421	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027424	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027425	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027427	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027428	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027431	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027432	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027433	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027436	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74027439	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74027441	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74027443	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053257	1.00[CHD][hapmap]
rs8192515	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs920037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs16941301	RBMXL3	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75656800-75667800	Weak transcription	Fetal Heart	heart
2	chr16:75657600-75666200	Weak transcription	Fetal Brain Male	brain
3	chr16:75657600-75668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:75658400-75679200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr16:75658400-75679800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:75658400-75679800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr16:75658600-75678200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr16:75658800-75672400	Strong transcription	Fetal Brain Female	brain
9	chr16:75658800-75672600	Strong transcription	GM12878-XiMat	blood
10	chr16:75658800-75677000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr16:75658800-75679800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr16:75659000-75671800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:75659000-75672000	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr16:75659000-75677000	Strong transcription	Brain Substantia Nigra	brain
15	chr16:75659000-75678200	Strong transcription	Fetal Muscle Leg	muscle
16	chr16:75659000-75678400	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr16:75659200-75675600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr16:75659200-75678000	Strong transcription	HepG2	liver
19	chr16:75659200-75680000	Strong transcription	Fetal Stomach	stomach
20	chr16:75659200-75680000	Strong transcription	A549	lung
21	chr16:75659200-75680600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr16:75659400-75668200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr16:75659400-75670600	Strong transcription	Brain Cingulate Gyrus	brain
24	chr16:75659400-75671400	Strong transcription	Fetal Lung	lung
25	chr16:75659400-75671800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr16:75659400-75671800	Strong transcription	Brain Germinal Matrix	brain
27	chr16:75659400-75672400	Strong transcription	Ovary	ovary
28	chr16:75659400-75674200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr16:75659400-75676800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr16:75659400-75677200	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr16:75659400-75678400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr16:75659400-75678400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr16:75659400-75679600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr16:75659400-75680000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr16:75659600-75666200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr16:75659600-75667400	Strong transcription	Gastric	stomach
37	chr16:75659600-75668400	Strong transcription	Right Ventricle	heart
38	chr16:75659600-75670400	Strong transcription	NHLF	lung
39	chr16:75659600-75671400	Strong transcription	Brain Anterior Caudate	brain
40	chr16:75659600-75671600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr16:75659600-75671600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr16:75659600-75671600	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr16:75659600-75672000	Strong transcription	Brain Angular Gyrus	brain
44	chr16:75659600-75672000	Strong transcription	NHEK	skin
45	chr16:75659600-75672400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr16:75659600-75675600	Strong transcription	HMEC	breast
47	chr16:75659600-75676800	Strong transcription	Left Ventricle	heart
48	chr16:75659600-75677000	Strong transcription	Brain Hippocampus Middle	brain
49	chr16:75659600-75678200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr16:75659600-75678200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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