Variant report

Variant	rs6842307
Chromosome Location	chr4:57328941-57328942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57328019-57329668	K562	blood:	n/a	n/a
2	POLR2A	chr4:57328046-57328950	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:57327632-57330405	GM12892	blood:	n/a	n/a
4	POLR2A	chr4:57328166-57329022	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:57326457-57334588	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:57328128-57329024	GM12892	blood:	n/a	n/a
7	POLR2A	chr4:57328023-57334626	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr4:57328095-57329011	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr4:57328727-57329753	K562	blood:	n/a	n/a
10	POLR2A	chr4:57328302-57328961	MCF-7	breast:	n/a	n/a
11	POLR2A	chr4:57328174-57331217	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:57327989-57328971	GM12892	blood:	n/a	n/a
13	POLR2A	chr4:57328260-57328986	U87	brain:	n/a	n/a
14	PML	chr4:57327978-57329019	K562	blood:	n/a	n/a
15	POLR2A	chr4:57327998-57328990	HepG2	liver:	n/a	n/a
16	POLR2A	chr4:57327841-57334590	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr4:57328020-57330417	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:57328712-57329004	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr4:57328083-57331197	A549	lung:	n/a	n/a
20	POLR2A	chr4:57321294-57335320	K562	blood:	n/a	n/a
21	POLR2A	chr4:57328117-57329577	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr4:57327796-57331218	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr4:57328291-57334478	K562	blood:	n/a	n/a
24	STAT3	chr4:57328722-57329005	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr4:57328107-57329027	GM12891	blood:	n/a	n/a
26	POLR2A	chr4:57328181-57330365	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr4:57328090-57334773	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:57328232-57329110	GM12891	blood:	n/a	n/a
29	POLR2A	chr4:57326028-57334384	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr4:57328069-57329068	GM12892	blood:	n/a	n/a
31	POLR2A	chr4:57328331-57329488	K562	blood:	n/a	n/a
32	POLR2A	chr4:57328913-57329151	K562	blood:	n/a	n/a
33	POLR2A	chr4:57328052-57329655	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:57302068..57304080-chr4:57328689..57330198,2	MCF-7	breast:
2	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
3	chr4:57310258..57311826-chr4:57327304..57329066,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPAT-1	chr4:57327536-57333761	NONHSAT096505

No data

Variant related genes	Relation type
SRP72	TF binding region
ENSG00000270109	TF binding region
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10009543	0.92[EUR][1000 genomes]
rs10015221	0.92[EUR][1000 genomes]
rs10866433	0.83[AFR][1000 genomes]
rs11610	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12646703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648503	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1356787	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17086793	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17086803	0.83[AFR][1000 genomes]
rs17086883	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17086887	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4383672	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4524447	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4615235	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4616819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865102	0.92[EUR][1000 genomes]
rs4865104	0.81[AFR][1000 genomes]
rs4865105	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4865110	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs57523479	0.90[ASN][1000 genomes]
rs58975286	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66599079	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs68101565	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6811482	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6816268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818715	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6819534	0.83[EUR][1000 genomes]
rs6820417	0.87[ASN][1000 genomes]
rs6830518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832168	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6848187	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7670198	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7689163	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7692073	0.92[EUR][1000 genomes]
rs7694047	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6842307	SRP72	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
2	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
3	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
4	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
5	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
6	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
7	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:57304400-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:57304400-57330800	Weak transcription	Brain Substantia Nigra	brain
10	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:57305800-57330400	Strong transcription	Fetal Thymus	thymus
12	chr4:57306200-57330200	Weak transcription	Brain Angular Gyrus	brain
13	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:57306600-57329400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:57306600-57330200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:57306600-57330400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:57306800-57330200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:57306800-57331000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:57307000-57330000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:57307200-57329600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:57307400-57329000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:57307400-57329400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr4:57307400-57329400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:57307400-57329400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:57307400-57329600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:57307400-57329800	Strong transcription	K562	blood
27	chr4:57307400-57330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:57308400-57329000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:57308800-57330000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:57309000-57330600	Weak transcription	Fetal Brain Male	brain
31	chr4:57313800-57329400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:57314000-57329200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:57314000-57330600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:57314400-57329200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr4:57314600-57329000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:57314600-57329000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr4:57314600-57329400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:57314600-57330200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:57314600-57330600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:57314600-57330800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:57314800-57329400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr4:57315000-57331800	Weak transcription	Aorta	Aorta
43	chr4:57315200-57329400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:57315600-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:57316000-57330200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:57316600-57330400	Strong transcription	Osteobl	bone
47	chr4:57316800-57329000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:57316800-57330200	Strong transcription	HSMM	muscle
49	chr4:57317200-57329000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:57317400-57329000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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