Variant report

Variant	rs3108551
Chromosome Location	chr19:37162125-37162126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37156941..37159491-chr19:37161171..37163007,2	MCF-7	breast:
2	chr19:37155855..37159234-chr19:37160019..37162576,3	MCF-7	breast:
3	chr19:37160578..37163087-chr19:37165819..37168377,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197808	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10411411	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1053064	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12162275	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12973307	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12981751	0.82[CEU][hapmap];0.96[AFR][1000 genomes]
rs2278168	0.83[TSI][hapmap]
rs2385640	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2462576	0.88[ASN][1000 genomes]
rs2912401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2912402	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2912406	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2912416	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2912417	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967424	0.89[EUR][1000 genomes]
rs2967455	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096621	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096626	0.83[EUR][1000 genomes]
rs3108169	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108170	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108175	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108180	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108198	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108199	0.94[EUR][1000 genomes]
rs3108200	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108210	0.84[TSI][hapmap]
rs3108213	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108220	0.85[ASN][1000 genomes]
rs3108547	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108558	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]
rs3108561	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]
rs3108571	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108578	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];0.92[TSI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108581	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108582	0.89[ASN][1000 genomes]
rs3108587	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108588	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3108595	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108599	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108601	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108611	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3111543	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3111545	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111546	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3745779	0.84[TSI][hapmap]
rs71337534	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7254978	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112546	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826979	0.84[ASN][1000 genomes]
rs826980	0.85[ASN][1000 genomes]
rs826986	0.84[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs865448	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3108551	ZNF529	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37158400-37169000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:37158600-37162800	Weak transcription	Brain Angular Gyrus	brain
3	chr19:37158600-37167400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:37158600-37167400	Weak transcription	Psoas Muscle	Psoas
5	chr19:37158600-37168800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:37158600-37168800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:37158600-37169000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:37158600-37169000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:37158600-37169000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:37158600-37172800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:37158600-37177200	Weak transcription	Fetal Kidney	kidney
12	chr19:37158600-37177400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:37158600-37177400	Weak transcription	NHDF-Ad	bronchial
14	chr19:37158600-37177800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:37158800-37166000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr19:37159000-37162400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:37159000-37177000	Weak transcription	NHLF	lung
18	chr19:37159200-37163800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:37159200-37163800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:37159200-37164600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:37159200-37164600	ZNF genes & repeats	Adipose Nuclei	Adipose
22	chr19:37159200-37165600	ZNF genes & repeats	Fetal Brain Female	brain
23	chr19:37159200-37166200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:37159200-37166200	ZNF genes & repeats	Liver	Liver
25	chr19:37159200-37168000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:37159200-37177600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr19:37159400-37162600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:37159400-37164000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:37159400-37177600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:37159600-37162200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:37159600-37162200	Weak transcription	Fetal Stomach	stomach
32	chr19:37159600-37162200	Weak transcription	Ovary	ovary
33	chr19:37159600-37162200	Weak transcription	Pancreas	Pancrea
34	chr19:37159600-37162400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:37159600-37162800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr19:37159600-37167000	Weak transcription	HSMM	muscle
37	chr19:37159600-37168800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr19:37159600-37168800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:37159600-37168800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:37159600-37168800	Weak transcription	HSMMtube	muscle
41	chr19:37159600-37169000	Weak transcription	Placenta	Placenta
42	chr19:37159600-37176200	Weak transcription	Gastric	stomach
43	chr19:37159600-37177400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:37159800-37162200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:37159800-37162200	Weak transcription	Right Ventricle	heart
46	chr19:37159800-37162400	Weak transcription	Colon Smooth Muscle	Colon
47	chr19:37159800-37162400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr19:37159800-37162800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:37159800-37168800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr19:37160000-37163800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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