Variant report

Variant	rs2516837
Chromosome Location	chr1:161014727-161014728
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	chr1:161014496-161017041	IMR90	lung:	n/a	n/a
2	IRF1	chr1:161014360-161016259	K562	blood:	n/a	chr1:161014773-161014787 chr1:161014776-161014790 chr1:161014770-161014784 chr1:161014779-161014793 chr1:161014777-161014790 chr1:161014775-161014789 chr1:161014779-161014789 chr1:161014773-161014794 chr1:161015569-161015582 chr1:161014771-161014791 chr1:161014765-161014785 chr1:161015780-161015794 chr1:161014777-161014790 chr1:161015568-161015588 chr1:161014769-161014783 chr1:161014772-161014781 chr1:161014774-161014785 chr1:161014777-161014790 chr1:161014777-161014791 chr1:161014779-161014790 chr1:161014778-161014795 chr1:161014780-161014791 chr1:161014773-161014783
3	POLR2A	chr1:161014571-161016485	HUVEC	blood vessel:	n/a	n/a
4	TAF1	chr1:161014664-161016386	H1-neurons	neurons:	n/a	n/a
5	NFATC1	chr1:161014571-161015225	GM12878	blood:	n/a	chr1:161014721-161014734
6	POLR2A	chr1:161014678-161018455	GM18505	blood:	n/a	n/a
7	IRF4	chr1:161014471-161015087	GM12878	blood:	n/a	chr1:161014773-161014794 chr1:161014777-161014791
8	TAF1	chr1:161014716-161015200	K562	blood:	n/a	n/a
9	POLR2A	chr1:161014712-161015480	K562	blood:	n/a	n/a
10	IKZF1	chr1:161014501-161015081	GM12878	blood:	n/a	n/a
11	CHD2	chr1:161014386-161015097	GM12878	blood:	n/a	n/a
12	NRF1	chr1:161014437-161016739	SK-N-SH	brain:	n/a	chr1:161015725-161015736 chr1:161015334-161015343
13	RCOR1	chr1:161014715-161016279	K562	blood:	n/a	n/a
14	SIN3AK20	chr1:161014635-161015835	K562	blood:	n/a	n/a
15	E2F6	chr1:161014694-161016384	A549	lung:	n/a	chr1:161015031-161015040 chr1:161015406-161015416
16	POLR2A	chr1:161014603-161018080	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:161014621-161016533	U87	brain:	n/a	n/a
18	POLR2A	chr1:161014375-161017763	GM12878	blood:	n/a	n/a
19	MTA3	chr1:161014325-161017601	GM12878	blood:	n/a	n/a
20	SPI1	chr1:161014682-161014982	K562	blood:	n/a	chr1:161014773-161014782 chr1:161014828-161014841 chr1:161014830-161014839 chr1:161014827-161014840
21	MTA3	chr1:161014514-161015278	GM12878	blood:	n/a	n/a
22	REST	chr1:161014624-161014926	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:161014475-161018415	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:161014572-161016454	K562	blood:	n/a	n/a
25	POU2F2	chr1:161014672-161015292	GM12891	blood:	n/a	chr1:161015030-161015038
26	MAX	chr1:161014677-161016247	K562	blood:	n/a	n/a
27	MAX	chr1:161014407-161015203	GM12878	blood:	n/a	n/a
28	SPI1	chr1:161014584-161015115	HL-60	blood:	n/a	chr1:161014773-161014782 chr1:161014828-161014841 chr1:161014830-161014839 chr1:161014827-161014840
29	TCF12	chr1:161014687-161015053	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:161014681-161016257	NB4	blood:	n/a	n/a
31	POLR2A	chr1:161014633-161015238	GM12892	blood:	n/a	n/a
32	POLR2A	chr1:161014643-161019294	GM12878	blood:	n/a	n/a
33	NRF1	chr1:161014510-161016222	GM12878	blood:	n/a	chr1:161015725-161015736 chr1:161015334-161015343
34	POLR2A	chr1:161014590-161016525	Raji	blood:	n/a	n/a
35	EP300	chr1:161014174-161015033	GM12878	blood:	n/a	chr1:161014768-161014782 chr1:161014218-161014227 chr1:161014774-161014788 chr1:161014885-161014894
36	YY1	chr1:161014704-161016663	GM12878	blood:	n/a	chr1:161016066-161016085 chr1:161015745-161015764 chr1:161015744-161015764 chr1:161015405-161015419 chr1:161015312-161015323 chr1:161015750-161015758 chr1:161016066-161016083 chr1:161016043-161016051 chr1:161015409-161015420 chr1:161015747-161015769 chr1:161016068-161016090 chr1:161015747-161015757 chr1:161016071-161016079 chr1:161016040-161016062
37	BHLHE40	chr1:161014558-161014776	HepG2	liver:	n/a	n/a
38	KAP1	chr1:161014617-161016401	HEK293	kidney:	n/a	n/a
39	SPI1	chr1:161014364-161015210	GM12878	blood:	n/a	chr1:161014773-161014782 chr1:161014828-161014841 chr1:161014830-161014839 chr1:161014827-161014840
40	SPI1	chr1:161014618-161014993	GM12878	blood:	n/a	chr1:161014773-161014782 chr1:161014828-161014841 chr1:161014830-161014839 chr1:161014827-161014840
41	JUND	chr1:161014704-161015169	K562	blood:	n/a	chr1:161014771-161014780
42	MXI1	chr1:161014011-161016561	SK-N-SH	brain:	n/a	chr1:161014433-161014448 chr1:161014431-161014446
43	POLR2A	chr1:161014609-161016364	PFSK-1	brain:	n/a	n/a
44	HEY1	chr1:161014721-161016316	HepG2	liver:	n/a	chr1:161015406-161015421
45	POLR2A	chr1:161014559-161018477	GM12878	blood:	n/a	n/a
46	TBL1XR1	chr1:161014437-161015331	GM12878	blood:	n/a	n/a
47	TEAD4	chr1:161014460-161015317	K562	blood:	n/a	n/a
48	PML	chr1:161014722-161014989	GM12878	blood:	n/a	n/a
49	SPI1	chr1:161014533-161015111	GM12891	blood:	n/a	chr1:161014773-161014782 chr1:161014828-161014841 chr1:161014830-161014839 chr1:161014827-161014840
50	SPI1	chr1:161014549-161015009	GM12891	blood:	n/a	chr1:161014773-161014782 chr1:161014828-161014841 chr1:161014830-161014839 chr1:161014827-161014840

No.	Distal block	Cell Line	Cell type
1	chr1:161013722..161017299-chr1:161066199..161071039,5	MCF-7	breast:
2	chr1:160990576..160992373-chr1:161014612..161018487,6	K562	blood:
3	chr1:161013470..161017562-chr1:161084888..161088962,4	MCF-7	breast:
4	chr1:160989663..160992818-chr1:161011844..161017868,15	MCF-7	breast:
5	chr1:161013542..161018278-chr1:161100825..161104206,7	MCF-7	breast:
6	chr1:161013435..161019346-chr1:161039308..161043996,7	MCF-7	breast:
7	chr1:161012196..161017661-chr1:161066183..161070852,8	MCF-7	breast:
8	chr1:161014200..161017793-chr1:161057956..161063190,6	MCF-7	breast:
9	chr1:161014674..161017488-chr19:12900939..12902636,2	MCF-7	breast:
10	chr1:161014274..161014774-chr16:67205347..67205849,2	Hela-S3	cervix:
11	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:
12	chr1:161013674..161020196-chr1:161084642..161090709,10	MCF-7	breast:
13	chr1:161011663..161014033-chr1:161014079..161015803,2	K562	blood:
14	chr1:161014566..161017528-chr1:161100154..161103523,4	K562	blood:
15	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
16	chr1:160989721..160993044-chr1:161014364..161019082,7	K562	blood:
17	chr1:161013921..161016040-chr1:161036662..161039623,2	MCF-7	breast:

Variant related genes	Relation type
USF1	TF binding region
ENSG00000158773	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000140939	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000186517	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11576837	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs12728349	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12748157	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073657	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[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]
rs2774273	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212386	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829791	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS 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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2516837	F11R	cis	parietal	SCAN
rs2516837	FCGR2A	cis	parietal	SCAN
rs2516837	APOA1BP	cis	cerebellum	SCAN
rs2516837	USF1	cis	multi-tissue	Pritchard
rs2516837	F11R	cis	cerebellum	SCAN
rs2516837	TOR2A	trans	parietal	SCAN
rs2516837	PEAR1	cis	cerebellum	SCAN
rs2516837	TSTD1	cis	Artery Tibial	GTEx
rs2516837	ITLN1	cis	cerebellum	SCAN
rs2516837	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161014000-161014800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:161014000-161014800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr1:161014000-161014800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:161014000-161014800	Flanking Active TSS	Fetal Brain Male	brain
5	chr1:161014000-161014800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:161014000-161014800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr1:161014000-161014800	Flanking Active TSS	HSMMtube	muscle
8	chr1:161014000-161014800	Flanking Active TSS	HUVEC	blood vessel
9	chr1:161014000-161014800	Flanking Active TSS	K562	blood
10	chr1:161014000-161014800	Flanking Active TSS	NH-A	brain
11	chr1:161014000-161015000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr1:161014000-161015200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr1:161014000-161015400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr1:161014000-161016200	Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:161014000-161016400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:161014000-161016400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:161014000-161017200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:161014200-161014800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:161014200-161014800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr1:161014200-161014800	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr1:161014200-161014800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:161014200-161014800	Flanking Active TSS	Liver	Liver
23	chr1:161014200-161014800	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr1:161014200-161014800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr1:161014200-161014800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr1:161014200-161015000	Flanking Active TSS	Hela-S3	cervix
27	chr1:161014200-161015200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr1:161014200-161016400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:161014200-161016400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:161014200-161016400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:161014200-161016400	Active TSS	Fetal Muscle Trunk	muscle
32	chr1:161014200-161016400	Active TSS	Lung	lung
33	chr1:161014200-161016400	Active TSS	Pancreas	Pancrea
34	chr1:161014200-161016600	Active TSS	H1 Cell Line	embryonic stem cell
35	chr1:161014200-161016600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:161014200-161016800	Active TSS	GM12878-XiMat	blood
37	chr1:161014400-161014800	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:161014400-161014800	Active TSS	Primary hematopoietic stem cells	blood
39	chr1:161014400-161014800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:161014400-161014800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
41	chr1:161014400-161015200	Active TSS	Right Atrium	heart
42	chr1:161014400-161015200	Transcr. at gene 5' and 3'	Dnd41	blood
43	chr1:161014400-161016000	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr1:161014400-161016000	Active TSS	Small Intestine	intestine
45	chr1:161014400-161016200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:161014400-161016200	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr1:161014400-161016200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:161014400-161016200	Active TSS	Fetal Intestine Large	intestine
49	chr1:161014400-161016200	Active TSS	Placenta	Placenta
50	chr1:161014400-161016200	Active TSS	Stomach Mucosa	stomach

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