Variant report

Variant	rs3108561
Chromosome Location	chr19:37184651-37184652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37178528..37181620-chr19:37184427..37188205,4	MCF-7	breast:
2	chr19:37180811..37182486-chr19:37182831..37185774,2	MCF-7	breast:
3	chr19:37178059..37180206-chr19:37184141..37185647,2	MCF-7	breast:
4	chr19:37184109..37186391-chr19:37262540..37264096,2	MCF-7	breast:
5	chr19:37177678..37180392-chr19:37181759..37186073,4	K562	blood:

Variant related genes	Relation type
ENSG00000267041	Chromatin interaction
ENSG00000267260	Chromatin interaction
ENSG00000189042	Chromatin interaction
ENSG00000225975	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1053064	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12162275	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12973307	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12981751	0.82[CEU][hapmap];0.91[AFR][1000 genomes]
rs2278168	0.87[TSI][hapmap]
rs2385640	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2462576	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2912401	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2912402	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2912406	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2912416	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2912417	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967424	0.86[EUR][1000 genomes]
rs2967455	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3096621	0.94[CEU][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3096626	0.81[EUR][1000 genomes]
rs3108169	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108170	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108175	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108180	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108199	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108200	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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];0.84[ASN][1000 genomes]
rs3108210	0.87[TSI][hapmap]
rs3108213	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108220	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3108547	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.82[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];0.84[MKK][hapmap];0.95[TSI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108553	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108554	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108558	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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108581	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108582	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3108587	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108588	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3108595	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108599	0.88[EUR][1000 genomes]
rs3108601	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108611	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108612	0.82[TSI][hapmap]
rs3111543	0.89[EUR][1000 genomes]
rs3111545	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3111546	0.89[EUR][1000 genomes]
rs3745779	0.87[TSI][hapmap]
rs71337534	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8112546	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs826979	0.90[ASN][1000 genomes]
rs826980	0.91[ASN][1000 genomes]
rs826986	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs865448	0.91[AFR][1000 genomes];0.95[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
rs3108561	FBXO17	cis	cerebellum	SCAN
rs3108561	RYR1	cis	cerebellum	SCAN
rs3108561	CIC	cis	cerebellum	SCAN
rs3108561	SARS2	cis	cerebellum	SCAN
rs3108561	GGN	cis	cerebellum	SCAN
rs3108561	ZNF529	Cis_1M	lymphoblastoid	RTeQTL
rs3108561	ZFP36	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37179400-37188200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr19:37179400-37188800	ZNF genes & repeats	Brain Germinal Matrix	brain
3	chr19:37179400-37194800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:37179400-37199200	Weak transcription	Fetal Heart	heart
5	chr19:37179600-37194400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:37179800-37186600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:37179800-37188800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:37179800-37188800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:37179800-37188800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:37179800-37188800	ZNF genes & repeats	Liver	Liver
11	chr19:37179800-37188800	ZNF genes & repeats	Fetal Brain Female	brain
12	chr19:37179800-37189000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr19:37179800-37189000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:37179800-37189200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:37180000-37186200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
16	chr19:37180000-37189200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:37180200-37185600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:37180200-37186000	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr19:37180200-37186000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
20	chr19:37180200-37186600	ZNF genes & repeats	Fetal Stomach	stomach
21	chr19:37180200-37187600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:37180200-37187800	ZNF genes & repeats	GM12878-XiMat	blood
23	chr19:37180200-37188400	Strong transcription	Placenta	Placenta
24	chr19:37180200-37188800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:37180200-37189000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:37180400-37185200	Strong transcription	Osteobl	bone
27	chr19:37180400-37186000	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr19:37180400-37186200	Strong transcription	Rectal Smooth Muscle	rectum
29	chr19:37180400-37186600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr19:37180400-37186600	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr19:37180400-37187000	Strong transcription	Stomach Smooth Muscle	stomach
32	chr19:37180400-37187600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:37180400-37188000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:37180400-37188200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:37180400-37188800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:37180400-37188800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:37180600-37188800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:37181400-37185000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:37181600-37185200	Strong transcription	Pancreatic Islets	Pancreatic Islet
40	chr19:37181600-37186000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:37181600-37188200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
42	chr19:37181600-37188800	ZNF genes & repeats	Adipose Nuclei	Adipose
43	chr19:37181600-37188800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
44	chr19:37181800-37186000	Strong transcription	Hela-S3	cervix
45	chr19:37181800-37187800	ZNF genes & repeats	Fetal Muscle Leg	muscle
46	chr19:37181800-37188600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
47	chr19:37181800-37188800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
48	chr19:37182000-37185400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:37182000-37186000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr19:37182000-37186400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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