Variant report

Variant	rs6875519
Chromosome Location	chr5:75842577-75842578
allele	A/C
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	MTA3	chr5:75842104-75844288	GM12878	blood:	n/a	n/a
2	CHD2	chr5:75842229-75844299	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:75842198-75842994	GM12891	blood:	n/a	n/a
4	CTCF	chr5:75842524-75842591	GM19239	blood:	n/a	n/a
5	SP1	chr5:75842196-75842973	GM12878	blood:	n/a	n/a
6	FOXM1	chr5:75842485-75843003	GM12878	blood:	n/a	n/a
7	SMC3	chr5:75842543-75842600	GM12878	blood:	n/a	n/a
8	RUNX3	chr5:75842189-75842906	GM12878	blood:	n/a	n/a
9	BHLHE40	chr5:75842244-75843807	GM12878	blood:	n/a	n/a
10	RELA	chr5:75842401-75843621	GM18505	blood:	n/a	n/a
11	BCLAF1	chr5:75842536-75843685	GM12878	blood:	n/a	chr5:75843310-75843319
12	NFATC1	chr5:75842251-75842839	GM12878	blood:	n/a	n/a
13	EGR1	chr5:75842547-75842801	K562	blood:	n/a	chr5:75842716-75842730
14	ELK1	chr5:75842464-75842672	GM12878	blood:	n/a	n/a
15	WRNIP1	chr5:75842424-75842922	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:75842572-75843906	GM12878	blood:	n/a	n/a
17	MTA3	chr5:75842283-75843064	GM12878	blood:	n/a	n/a
18	IRF4	chr5:75842330-75842988	GM12878	blood:	n/a	n/a
19	RUNX3	chr5:75842112-75843749	GM12878	blood:	n/a	chr5:75843370-75843379 chr5:75843370-75843379
20	TCF3	chr5:75842120-75842965	GM12878	blood:	n/a	n/a
21	TBP	chr5:75842238-75843640	GM12878	blood:	n/a	n/a
22	CREB1	chr5:75842171-75843766	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr5:75842254-75843581	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:75842276-75843059	GM12892	blood:	n/a	n/a
25	TCF12	chr5:75842292-75842842	GM12878	blood:	n/a	n/a
26	POU2F2	chr5:75842504-75842923	GM12878	blood:	n/a	n/a
27	PML	chr5:75842413-75843762	GM12878	blood:	n/a	n/a
28	NFIC	chr5:75842272-75843807	GM12878	blood:	n/a	n/a
29	MXI1	chr5:75842230-75843966	GM12878	blood:	n/a	n/a
30	MAX	chr5:75842383-75843905	GM12878	blood:	n/a	n/a
31	POLR2A	chr5:75842274-75843535	GM12878	blood:	n/a	n/a
32	POU2F2	chr5:75842501-75842935	GM12891	blood:	n/a	n/a
33	EP300	chr5:75842280-75842933	GM12878	blood:	n/a	chr5:75842431-75842445
34	PAX5	chr5:75842107-75843023	GM12878	blood:	n/a	chr5:75842697-75842706 chr5:75842793-75842803 chr5:75842758-75842767 chr5:75842431-75842440 chr5:75842444-75842453
35	FOXA1	chr5:75842559-75843079	HepG2	liver:	n/a	n/a
36	ATF2	chr5:75842225-75843735	GM12878	blood:	n/a	n/a
37	RCOR1	chr5:75842337-75843982	GM12878	blood:	n/a	n/a
38	SP1	chr5:75842137-75842944	GM12878	blood:	n/a	n/a
39	NRF1	chr5:75842392-75842630	GM12878	blood:	n/a	n/a
40	EP300	chr5:75842174-75843737	GM12878	blood:	n/a	chr5:75842431-75842445
41	POLR2A	chr5:75842228-75843863	GM12878	blood:	n/a	n/a
42	CREB1	chr5:75842110-75843015	GM12878	blood:	n/a	n/a
43	EP300	chr5:75842171-75843681	GM12878	blood:	n/a	chr5:75842431-75842445
44	POLR2A	chr5:75842273-75843040	GM12891	blood:	n/a	n/a
45	ZNF384	chr5:75842228-75842936	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
IQGAP2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10055118	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064543	0.82[TSI][hapmap]
rs10072548	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12109754	0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12657065	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3797376	0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62361995	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6893849	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710523	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7735089	0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9293688	0.82[TSI][hapmap]

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	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6875519	TMEM171	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:75837400-75842800	Enhancers	Liver	Liver
3	chr5:75839400-75842600	Weak transcription	Thymus	Thymus
4	chr5:75839600-75845400	Enhancers	HepG2	liver
5	chr5:75839600-75845800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:75839600-75846000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr5:75840000-75842600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr5:75840200-75842600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr5:75840200-75842800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:75840200-75842800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr5:75840200-75842800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr5:75840200-75842800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:75840200-75842800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:75840200-75843200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:75840400-75842800	Enhancers	Primary hematopoietic stem cells	blood
16	chr5:75840400-75843000	Weak transcription	Fetal Intestine Large	intestine
17	chr5:75840400-75843600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:75840600-75842600	Weak transcription	Fetal Lung	lung
19	chr5:75840600-75843000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:75841000-75843200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:75841200-75842600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:75841200-75843000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr5:75841400-75842800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:75841800-75842800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr5:75841800-75843000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr5:75841800-75843000	Enhancers	Primary B cells from cord blood	blood
27	chr5:75842000-75842600	Enhancers	Esophagus	oesophagus
28	chr5:75842000-75842600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr5:75842000-75842800	Enhancers	Duodenum Mucosa	Duodenum
30	chr5:75842000-75843000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:75842000-75843800	Enhancers	Fetal Muscle Leg	muscle
32	chr5:75842000-75844600	Enhancers	Primary B cells from peripheral blood	blood
33	chr5:75842000-75845800	Enhancers	Stomach Mucosa	stomach
34	chr5:75842200-75842800	Enhancers	Primary T cells from cord blood	blood
35	chr5:75842200-75843400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr5:75842200-75843400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:75842200-75843600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:75842200-75843600	Enhancers	Pancreas	Pancrea
39	chr5:75842200-75843800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr5:75842200-75844200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr5:75842200-75844400	Enhancers	Fetal Thymus	thymus
42	chr5:75842200-75844600	Flanking Active TSS	GM12878-XiMat	blood
43	chr5:75842200-75844800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:75842200-75845800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr5:75842400-75842600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:75842400-75842800	Enhancers	Colonic Mucosa	Colon
47	chr5:75842400-75842800	Enhancers	Spleen	Spleen
48	chr5:75842400-75843000	Enhancers	Brain Anterior Caudate	brain
49	chr5:75842400-75843000	Enhancers	Lung	lung
50	chr5:75842400-75843000	Active TSS	Rectal Mucosa Donor 29	rectum

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