Variant report

Variant	rs3108558
Chromosome Location	chr19:37179123-37179124
allele	A/G
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	chr19:37177666-37179223	SK-N-MC	brain:	n/a	n/a
2	PML	chr19:37177913-37179316	GM12878	blood:	n/a	chr19:37178699-37178707
3	POLR2A	chr19:37177657-37179177	MCF10A-Er-Src	breast:	n/a	n/a
4	ZKSCAN1	chr19:37178195-37179264	Hela-S3	cervix:	n/a	n/a
5	SMC3	chr19:37177954-37179284	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:37179013-37179152	K562	blood:	n/a	n/a
7	POLR2A	chr19:37178011-37179139	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr19:37178057-37179229	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr19:37177335-37179237	SK-N-SH	brain:	n/a	n/a
10	USF1	chr19:37178223-37179293	A549	lung:	n/a	n/a
11	MAX	chr19:37177740-37179362	Hela-S3	cervix:	n/a	chr19:37179110-37179119
12	POLR2A	chr19:37178048-37179141	GM12878	blood:	n/a	n/a
13	USF2	chr19:37179045-37179265	Hela-S3	cervix:	n/a	n/a
14	MAX	chr19:37177620-37179363	A549	lung:	n/a	chr19:37179110-37179119
15	HCFC1	chr19:37177383-37179323	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr19:37177802-37179165	Hela-S3	cervix:	n/a	n/a
17	GATA3	chr19:37177896-37179229	A549	lung:	n/a	n/a
18	TCF12	chr19:37177468-37179257	A549	lung:	n/a	chr19:37178474-37178481 chr19:37178712-37178722
19	MAX	chr19:37177836-37179160	A549	lung:	n/a	chr19:37179110-37179119
20	ZNF263	chr19:37177316-37179318	HEK293-T-REx	kidney:	n/a	n/a
21	SREBP1	chr19:37177853-37179213	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr19:37177881-37179236	MCF-7	breast:	n/a	n/a
23	SIX5	chr19:37177850-37179125	A549	lung:	n/a	chr19:37178392-37178401 chr19:37178394-37178403 chr19:37178391-37178405
24	REST	chr19:37177773-37179178	A549	lung:	n/a	chr19:37178536-37178549
25	SIN3AK20	chr19:37177805-37179217	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:37177766..37179816-chr19:37265277..37267800,2	MCF-7	breast:
2	chr19:37038036..37040830-chr19:37176881..37179372,3	MCF-7	breast:
3	chr17:45973368..45973979-chr19:37178763..37179345,2	Hela-S3	cervix:
4	chr19:37157483..37161085-chr19:37175435..37180024,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225975	TF binding region
ZNF567	TF binding region
ENSG00000197808	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000267353	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10411411	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1053064	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12162275	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12973307	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12981751	0.83[CEU][hapmap];0.93[AFR][1000 genomes]
rs2278168	0.87[TSI][hapmap]
rs2385640	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2462576	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2912401	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2912402	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2912406	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2912416	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2912417	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967424	0.86[EUR][1000 genomes]
rs2967455	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967470	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3096621	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3096626	0.81[EUR][1000 genomes]
rs3108169	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108170	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108175	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108180	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108198	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108199	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108200	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108207	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108210	0.87[TSI][hapmap]
rs3108213	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108220	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3108547	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108548	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108551	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108553	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108554	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108561	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[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108571	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108581	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108582	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3108587	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108588	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3108595	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108599	0.88[EUR][1000 genomes]
rs3108601	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108611	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108612	0.82[TSI][hapmap]
rs3111543	0.89[EUR][1000 genomes]
rs3111545	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111546	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3745779	0.87[TSI][hapmap]
rs71337534	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7254978	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];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8112546	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826979	0.89[ASN][1000 genomes]
rs826980	0.89[ASN][1000 genomes]
rs826986	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs865448	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers 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	73 gene(s)	inside rSNPs	diseases
7	esv3492171	chr19:37122012-37190210	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
8	esv3492172	chr19:37122562-37190060	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
9	esv3492173	chr19:37122562-37190060	Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
10	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	esv3420176	chr19:37130161-37207917	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
13	nsv1061250	chr19:37134068-37188771	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
14	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv470139	chr19:37171201-37264190	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3108558	RYR1	cis	cerebellum	SCAN
rs3108558	ZFP36	cis	cerebellum	SCAN
rs3108558	GGN	cis	cerebellum	SCAN
rs3108558	SARS2	cis	cerebellum	SCAN
rs3108558	CIC	cis	cerebellum	SCAN
rs3108558	ZNF529	Cis_1M	lymphoblastoid	RTeQTL
rs3108558	FBXO17	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37177000-37179400	Active TSS	HSMMtube	muscle
2	chr19:37177000-37179400	Active TSS	NHLF	lung
3	chr19:37177200-37179200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:37177200-37179400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:37177200-37179400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr19:37177200-37179600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:37177200-37180000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:37177200-37180200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr19:37177400-37179200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr19:37177400-37179200	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr19:37177400-37179400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:37177400-37179400	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr19:37177400-37179400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:37177400-37179400	Active TSS	Fetal Intestine Large	intestine
15	chr19:37177400-37179400	Active TSS	GM12878-XiMat	blood
16	chr19:37177400-37179600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr19:37177400-37180000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:37177400-37180000	Active TSS	HSMM	muscle
19	chr19:37177600-37179200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr19:37177600-37179200	Bivalent/Poised TSS	HepG2	liver
21	chr19:37177600-37179400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr19:37177600-37179400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:37177600-37179400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:37177600-37179400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:37177600-37179400	Active TSS	K562	blood
26	chr19:37177600-37179600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:37177600-37179600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:37177800-37179200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr19:37177800-37179200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:37177800-37179200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:37177800-37179200	Active TSS	Esophagus	oesophagus
32	chr19:37177800-37179200	Active TSS	Small Intestine	intestine
33	chr19:37177800-37179400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr19:37177800-37179400	Active TSS	Muscle Satellite Cultured Cells	--
35	chr19:37177800-37179600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:37177800-37179600	Active TSS	Fetal Intestine Small	intestine
37	chr19:37177800-37179600	Active TSS	HMEC	breast
38	chr19:37177800-37180000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:37178000-37179200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:37178000-37179200	Active TSS	Left Ventricle	heart
41	chr19:37178000-37179200	Active TSS	Pancreas	Pancrea
42	chr19:37178000-37179400	Active TSS	Brain Cingulate Gyrus	brain
43	chr19:37178000-37179400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:37178000-37179400	Active TSS	Colonic Mucosa	Colon
45	chr19:37178000-37179400	Active TSS	Psoas Muscle	Psoas
46	chr19:37178000-37179400	Active TSS	Osteobl	bone
47	chr19:37178000-37179600	Active TSS	Hela-S3	cervix
48	chr19:37178000-37179800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:37178200-37179200	Active TSS	Lung	lung
50	chr19:37178200-37179400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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