Variant report

Variant	rs10416908
Chromosome Location	chr19:55900132-55900133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55895189-55904986	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:55896221-55905168	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:55899723-55900435	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:55894809-55904996	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:55900090-55902882	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:55899903-55905128	IMR90	lung:	n/a	n/a
7	POLR2A	chr19:55898959-55905063	A549	lung:	n/a	n/a
8	POLR2A	chr19:55900001-55900439	A549	lung:	n/a	n/a
9	POLR2A	chr19:55899718-55903096	GM12891	blood:	n/a	n/a
10	POLR2A	chr19:55900038-55905067	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr19:55894841-55904473	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:55895220-55903350	K562	blood:	n/a	n/a
13	POLR2A	chr19:55895580-55900320	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr19:55895906-55903362	K562	blood:	n/a	n/a
15	POLR2A	chr19:55896728-55903901	GM12892	blood:	n/a	n/a
16	RCOR1	chr19:55900061-55900252	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:55900032-55900406	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:55899999-55903358	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:55896275-55903749	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr19:55899716-55903100	GM12891	blood:	n/a	n/a
21	POLR2A	chr19:55900056-55905085	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr19:55897004-55902318	HL-60	blood:	n/a	n/a
23	POLR2A	chr19:55899960-55903344	GM18951	blood:	n/a	n/a
24	POLR2A	chr19:55899095-55903608	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr19:55896334-55903301	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:55899268-55902332	K562	blood:	n/a	n/a
27	POLR2A	chr19:55900003-55903739	GM19099	blood:	n/a	n/a
28	POLR2A	chr19:55894561-55904659	K562	blood:	n/a	n/a
29	POLR2A	chr19:55896138-55903881	GM12892	blood:	n/a	n/a
30	POLR2A	chr19:55899536-55900355	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr19:55894840-55903086	K562	blood:	n/a	n/a
32	POLR2A	chr19:55894680-55903724	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr19:55900106-55902249	GM12892	blood:	n/a	n/a
34	CHD1	chr19:55896302-55901705	IMR90	lung:	n/a	chr19:55897281-55897291
35	POLR2A	chr19:55898628-55900458	GM12878	blood:	n/a	n/a
36	POLR2A	chr19:55895228-55904984	GM12891	blood:	n/a	n/a
37	POLR2A	chr19:55896380-55904806	U87	brain:	n/a	n/a
38	POLR2A	chr19:55899864-55903122	GM18526	blood:	n/a	n/a
39	POLR2A	chr19:55900071-55904589	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr19:55900073-55902245	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:55899798-55903585	U87	brain:	n/a	n/a
42	POLR2A	chr19:55900119-55900422	ProgFib	skin:	n/a	n/a
43	POLR2A	chr19:55899659-55904089	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr19:55899912-55900362	HepG2	liver:	n/a	n/a
45	POLR2A	chr19:55896741-55903157	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:55895466-55904599	HepG2	liver:	n/a	n/a
47	POLR2A	chr19:55896365-55903981	K562	blood:	n/a	n/a
48	POLR2A	chr19:55898841-55903147	GM12891	blood:	n/a	n/a
49	POLR2A	chr19:55895837-55905107	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr19:55900106-55900345	A549	lung:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55822211..55824840-chr19:55897185..55900181,3	MCF-7	breast:
2	chr19:55894730..55901388-chr19:55970612..55975937,9	K562	blood:
3	chr19:55811782..55819446-chr19:55894353..55900958,7	K562	blood:
4	chr19:55764902..55773441-chr19:55891413..55900303,21	K562	blood:
5	chr19:55724006..55730191-chr19:55893749..55903961,17	K562	blood:
6	chr19:55736940..55740249-chr19:55897225..55900387,3	K562	blood:
7	chr19:55767441..55773483-chr19:55893952..55900251,14	MCF-7	breast:
8	chr12:46384045..46384980-chr19:55899620..55900478,2	Hela-S3	cervix:
9	chr19:55848515..55857343-chr19:55894079..55900232,19	MCF-7	breast:
10	chr19:55897327..55900767-chr19:56164045..56167151,4	K562	blood:
11	chr19:55790067..55793851-chr19:55895113..55900809,14	K562	blood:
12	chr19:55763551..55774813-chr19:55891413..55900376,23	K562	blood:
13	chr19:55723991..55730191-chr19:55895529..55902666,13	K562	blood:
14	chr14:90863107..90863847-chr19:55899956..55900926,2	HCT-116	colon:
15	chr19:55790075..55793363-chr19:55895323..55900809,10	K562	blood:
16	chr19:55897252..55900237-chr19:55952546..55954535,2	K562	blood:
17	chr19:55899260..55901046-chr19:55971490..55973402,2	K562	blood:
18	chr19:55808885..55818962-chr19:55893792..55900928,16	MCF-7	breast:
19	chr19:55847613..55856135-chr19:55893756..55900268,15	K562	blood:

No data

Variant related genes	Relation type
TMEM238	TF binding region
ENSG00000160469	Chromatin interaction
ENSG00000198668	Chromatin interaction
ENSG00000268729	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000180089	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000269808	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000187902	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10403564	0.89[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403989	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404370	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405802	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408088	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408448	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408525	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408540	0.89[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410269	0.87[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10411984	0.82[LWK][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs10415365	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420818	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes]
rs10421889	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423589	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424652	0.89[ASW][hapmap];1.00[CHB][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425107	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425362	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425596	0.93[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs10426959	1.00[MEX][hapmap]
rs28408730	0.98[AFR][1000 genomes]
rs28536711	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28540780	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28797308	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4252548	1.00[CHB][hapmap]
rs59698058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61468173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617871	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617888	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617896	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619651	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
4	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
5	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
6	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
7	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
8	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
9	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
10	nsv516199	chr19:55854313-55901099	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
12	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
13	nsv544085	chr19:55875808-55911275	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10416908	RPL28	cis	multi-tissue	Pritchard
rs10416908	RPL28	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55897400-55900200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
2	chr19:55897400-55900200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:55897400-55900400	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr19:55897600-55900200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr19:55897600-55900400	Transcr. at gene 5' and 3'	NHEK	skin
6	chr19:55897600-55901000	Transcr. at gene 5' and 3'	A549	lung
7	chr19:55897600-55903000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:55897800-55900200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
9	chr19:55897800-55900600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
10	chr19:55897800-55900800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:55897800-55901400	Transcr. at gene 5' and 3'	Hela-S3	cervix
12	chr19:55897800-55902200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:55897800-55903000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:55898000-55900200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:55898000-55900200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:55898000-55900200	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
17	chr19:55898000-55900400	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
18	chr19:55898000-55900400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
19	chr19:55898000-55900400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
20	chr19:55898000-55900600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:55898000-55901400	Transcr. at gene 5' and 3'	K562	blood
22	chr19:55898000-55901800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:55898200-55900200	Transcr. at gene 5' and 3'	Osteobl	bone
24	chr19:55898200-55900400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
25	chr19:55898200-55900600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
26	chr19:55898200-55900600	Transcr. at gene 5' and 3'	NHLF	lung
27	chr19:55898200-55901000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:55898400-55900200	Transcr. at gene 5' and 3'	NH-A	brain
29	chr19:55898400-55900400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
30	chr19:55898400-55900400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
31	chr19:55898400-55900400	Transcr. at gene 5' and 3'	HSMM	muscle
32	chr19:55898400-55900800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr19:55898400-55901200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
34	chr19:55898600-55900200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:55898600-55900200	Genic enhancers	Left Ventricle	heart
36	chr19:55898600-55900400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
37	chr19:55898600-55900800	Genic enhancers	Liver	Liver
38	chr19:55898600-55902200	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr19:55898600-55902200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:55898800-55900200	Genic enhancers	Primary B cells from cord blood	blood
41	chr19:55898800-55900200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr19:55898800-55900200	Enhancers	Fetal Heart	heart
43	chr19:55898800-55900400	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr19:55898800-55901000	Enhancers	Right Atrium	heart
45	chr19:55898800-55901200	Genic enhancers	Placenta	Placenta
46	chr19:55898800-55901800	Genic enhancers	Fetal Brain Male	brain
47	chr19:55898800-55903000	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr19:55899000-55900200	Genic enhancers	Small Intestine	intestine
49	chr19:55899000-55900600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr19:55899000-55900600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood

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