Variant report

Variant	rs12975981
Chromosome Location	chr19:21591358-21591359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21584484..21588831-chr19:21589336..21593568,7	K562	blood:
2	chr19:21578623..21581183-chr19:21590706..21592354,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196268	Chromatin interaction
ENSG00000269237	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1012040	0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs10406824	1.00[JPT][hapmap]
rs11085455	0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11673406	0.83[EUR][1000 genomes]
rs12150996	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12151067	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151068	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151222	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12971724	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12981869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984238	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1500400	1.00[JPT][hapmap]
rs1500401	1.00[JPT][hapmap]
rs1520073	1.00[JPT][hapmap]
rs1533675	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1607664	0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1678822	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs17618715	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17618778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1762580	0.85[ASN][1000 genomes]
rs17680671	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs1813234	0.86[CEU][hapmap]
rs1984771	1.00[JPT][hapmap]
rs2133816	1.00[JPT][hapmap]
rs2133820	0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2170024	1.00[YRI][hapmap]
rs2173724	1.00[JPT][hapmap]
rs2173728	0.80[EUR][1000 genomes]
rs2246914	0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2262896	0.80[EUR][1000 genomes]
rs2358984	0.86[CEU][hapmap]
rs2562399	1.00[JPT][hapmap]
rs2562448	1.00[JPT][hapmap]
rs2562457	1.00[JPT][hapmap]
rs2562458	1.00[JPT][hapmap]
rs2650779	1.00[JPT][hapmap]
rs2650780	1.00[JPT][hapmap]
rs2650781	0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2650783	1.00[JPT][hapmap]
rs2650791	1.00[JPT][hapmap]
rs2650794	1.00[JPT][hapmap]
rs2650799	1.00[JPT][hapmap]
rs2650810	0.83[EUR][1000 genomes]
rs2650845	1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2650847	0.82[EUR][1000 genomes]
rs2681371	1.00[JPT][hapmap]
rs2681372	1.00[JPT][hapmap]
rs28839521	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2914629	0.83[EUR][1000 genomes]
rs2914636	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2914637	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2914638	1.00[YRI][hapmap]
rs2914647	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2928210	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34560125	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34875588	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35148123	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35578515	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35860067	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4341872	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4461198	0.84[EUR][1000 genomes]
rs483383	0.85[ASN][1000 genomes]
rs488125	0.86[CEU][hapmap];0.89[YRI][hapmap]
rs501647	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[ASN][1000 genomes]
rs504280	0.82[CEU][hapmap];0.80[YRI][hapmap]
rs509540	0.86[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs514390	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs549882	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs552039	0.85[ASN][1000 genomes]
rs56152627	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs566230	0.86[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs57055133	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57841525	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58121117	0.85[ASN][1000 genomes]
rs59617671	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs608002	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62107470	0.85[ASN][1000 genomes]
rs62107538	0.85[ASN][1000 genomes]
rs62109224	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62110379	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62111469	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62111470	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62111476	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs629548	1.00[JPT][hapmap]
rs6511247	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs669046	1.00[JPT][hapmap]
rs670813	0.85[ASN][1000 genomes]
rs67723811	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs685844	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7245848	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7246684	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7248700	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7249636	0.86[CEU][hapmap]
rs7254436	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs7254762	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs7257584	0.81[ASN][1000 genomes]
rs7258211	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7259178	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73025767	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8099863	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8100318	1.00[JPT][hapmap]
rs8101077	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8102655	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8102854	1.00[JPT][hapmap]
rs8103151	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8103417	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8105404	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8105629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8107042	0.81[EUR][1000 genomes]
rs8107940	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8107999	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs8111189	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8113558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880896	0.84[CHD][hapmap]
rs939301	0.84[CHD][hapmap]

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	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv578953	chr19:21586797-21609607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
16	nsv578954	chr19:21587261-21604510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12975981	ZNF493	cis	lymphoblastoid	seeQTL
rs12975981	ZNF429	cis	Artery Aorta	GTEx
rs12975981	ZNF429	cis	cerebellum	SCAN
rs12975981	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs12975981	PLA2G10	trans	cerebellum	SCAN
rs12975981	ZNF493	cis	multi-tissue	Pritchard
rs12975981	ARMC6	cis	cerebellum	SCAN
rs12975981	ZNF429	cis	parietal	SCAN
rs12975981	ZNF429	cis	Whole Blood	GTEx
rs12975981	ZNF493	cis	cerebellum	SCAN
rs12975981	ZNF738	cis	parietal	SCAN
rs12975981	ZNF738	cis	Adipose Subcutaneous	GTEx
rs12975981	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs12975981	ZNF738	cis	cerebellum	SCAN
rs12975981	ZNF100	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21580600-21592600	Weak transcription	Placenta	Placenta
2	chr19:21580600-21593200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:21580600-21593600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:21580600-21600200	Weak transcription	Gastric	stomach
5	chr19:21580600-21602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:21580800-21595400	Weak transcription	HUVEC	blood vessel
7	chr19:21581000-21591800	Weak transcription	Pancreas	Pancrea
8	chr19:21581000-21596200	Weak transcription	Aorta	Aorta
9	chr19:21581000-21598800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:21581400-21592000	Weak transcription	NH-A	brain
11	chr19:21581400-21594600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:21581400-21596800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr19:21581400-21598800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:21581600-21591800	Weak transcription	Right Ventricle	heart
15	chr19:21581600-21592200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr19:21581600-21592400	Weak transcription	Brain Angular Gyrus	brain
17	chr19:21581600-21592400	Weak transcription	Fetal Kidney	kidney
18	chr19:21581600-21594600	Weak transcription	HepG2	liver
19	chr19:21581600-21601800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:21583800-21592200	Weak transcription	Brain Anterior Caudate	brain
22	chr19:21583800-21595600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr19:21583800-21596200	Weak transcription	Brain Substantia Nigra	brain
24	chr19:21583800-21598200	Weak transcription	Fetal Brain Male	brain
25	chr19:21584000-21591800	Weak transcription	Osteobl	bone
26	chr19:21584000-21592200	Weak transcription	HSMMtube	muscle
27	chr19:21584000-21596200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:21584000-21596200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr19:21584000-21597400	Weak transcription	Colon Smooth Muscle	Colon
30	chr19:21584400-21592800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:21584800-21598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:21585000-21596800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
33	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:21585200-21592200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr19:21585200-21592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:21585200-21594200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:21585400-21592000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:21586000-21591800	Weak transcription	Left Ventricle	heart
39	chr19:21586000-21594800	Weak transcription	Psoas Muscle	Psoas
40	chr19:21586000-21599400	Weak transcription	Spleen	Spleen
41	chr19:21586200-21591800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:21586200-21592800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr19:21586400-21592000	Weak transcription	HSMM	muscle
44	chr19:21586600-21596200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:21586800-21598400	Weak transcription	Colonic Mucosa	Colon
46	chr19:21587200-21592200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr19:21587400-21592800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr19:21587800-21591400	Strong transcription	Primary T cells from cord blood	blood
49	chr19:21587800-21593000	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr19:21588000-21592800	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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