Variant report

Variant	rs17224674
Chromosome Location	chr12:48596579-48596580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48591422..48593721-chr12:48594349..48596928,3	MCF-7	breast:
2	chr12:48418539..48420191-chr12:48595608..48598283,2	K562	blood:

Variant related genes	Relation type
ENSG00000269514	Chromatin interaction
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1004746	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1004806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10128967	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs10506276	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10506277	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506278	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs10506280	0.87[AMR][1000 genomes]
rs11830378	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11830864	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11833380	0.89[AMR][1000 genomes]
rs11834109	1.00[CEU][hapmap]
rs11837419	0.89[AMR][1000 genomes]
rs11837548	0.89[AMR][1000 genomes]
rs11837571	0.89[AMR][1000 genomes]
rs12297820	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs12301562	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs17122802	0.87[EUR][1000 genomes]
rs17122906	0.87[AMR][1000 genomes]
rs17122918	1.00[CEU][hapmap]
rs17122920	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17224828	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17225198	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes]
rs17225261	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17225366	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17225751	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17226359	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17226506	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17226723	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17607800	0.82[TSI][hapmap]
rs17823193	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17823313	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17823415	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17823565	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes]
rs17824200	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17824705	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17824989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs17825013	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2228501	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3936179	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4075914	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41291959	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41291961	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55638557	0.89[AMR][1000 genomes]
rs55654871	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55682541	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55707383	0.84[EUR][1000 genomes]
rs55752728	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55763362	0.87[AMR][1000 genomes]
rs55794326	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55854069	0.87[AMR][1000 genomes]
rs55886138	0.81[EUR][1000 genomes]
rs55890195	0.96[EUR][1000 genomes]
rs55894137	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55920439	0.87[AMR][1000 genomes]
rs55945889	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55953382	0.84[EUR][1000 genomes]
rs56049209	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56084718	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56110736	0.87[AMR][1000 genomes]
rs56116946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56187356	0.96[EUR][1000 genomes]
rs56205628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56271815	0.87[AMR][1000 genomes]
rs56288528	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56378908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56383074	0.87[AMR][1000 genomes]
rs56389692	0.87[AMR][1000 genomes]
rs56412095	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6580666	0.87[AMR][1000 genomes]
rs7138353	0.89[AMR][1000 genomes]
rs7297558	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes]
rs7301153	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs7301509	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs7307383	0.89[AMR][1000 genomes]
rs7307676	0.89[AMR][1000 genomes]
rs7307874	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs7310715	0.89[AMR][1000 genomes]
rs7310935	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs73304917	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74089155	0.96[EUR][1000 genomes]
rs74089159	0.85[EUR][1000 genomes]
rs74089163	0.85[EUR][1000 genomes]
rs751315	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs751316	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv976031	chr12:48594968-48610975	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv976038	chr12:48596152-48610975	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17224674	ZNF641	cis	multi-tissue	Pritchard
rs17224674	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48592800-48600400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48593000-48596600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:48593200-48596800	Weak transcription	Brain Substantia Nigra	brain
4	chr12:48593200-48599000	Weak transcription	Brain Angular Gyrus	brain
5	chr12:48593200-48600200	Weak transcription	Right Ventricle	heart
6	chr12:48593400-48600800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:48593600-48596600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:48593800-48596600	Weak transcription	Left Ventricle	heart
9	chr12:48593800-48598400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:48593800-48598400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:48594000-48596800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr12:48594000-48598400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:48594200-48598600	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:48594200-48598800	Weak transcription	Fetal Heart	heart
15	chr12:48594400-48596800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
16	chr12:48594600-48596600	Weak transcription	Right Atrium	heart
17	chr12:48594600-48596800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:48594800-48599000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:48595000-48598400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:48595000-48598400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:48595200-48597600	Weak transcription	Brain Anterior Caudate	brain
22	chr12:48595200-48598600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:48595200-48598600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:48595200-48598800	Weak transcription	Fetal Lung	lung
25	chr12:48595200-48600400	Weak transcription	Psoas Muscle	Psoas
26	chr12:48595600-48596600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:48595600-48609600	Weak transcription	Placenta	Placenta
28	chr12:48595800-48596600	Weak transcription	Primary T cells from cord blood	blood
29	chr12:48595800-48599600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:48595800-48600800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:48596000-48596600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr12:48596000-48596600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
33	chr12:48596000-48596800	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr12:48596000-48597000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr12:48596000-48597000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:48596000-48597000	Enhancers	Lung	lung
37	chr12:48596000-48597200	ZNF genes & repeats	Gastric	stomach
38	chr12:48596000-48599600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:48596200-48596600	Weak transcription	Ovary	ovary
40	chr12:48596200-48598400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr12:48596400-48597000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:48596400-48597200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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