Variant report

Variant	rs10506276
Chromosome Location	chr12:48594514-48594515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48593487..48595723-chr12:48689162..48691231,3	K562	blood:
2	chr12:48591422..48593721-chr12:48594349..48596928,3	MCF-7	breast:
3	chr12:48366898..48369197-chr12:48592697..48594577,2	K562	blood:

Variant related genes	Relation type
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1004746	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs1004806	0.87[EUR][1000 genomes]
rs10128967	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10506277	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10506278	0.85[CEU][hapmap]
rs10875718	1.00[CHB][hapmap]
rs10875719	1.00[CHB][hapmap]
rs11830378	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830617	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830864	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833380	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834109	0.85[CEU][hapmap]
rs11835509	1.00[ASN][1000 genomes]
rs11837419	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837548	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837571	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297820	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12301562	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs17122802	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122918	0.85[CEU][hapmap]
rs17122920	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs17224674	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs17224828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17225198	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17225261	0.81[CEU][hapmap]
rs17225751	0.85[CEU][hapmap]
rs17226359	0.85[CEU][hapmap]
rs17226506	0.85[CEU][hapmap]
rs17226723	0.85[CEU][hapmap]
rs17823193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823313	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823565	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824705	0.85[CEU][hapmap]
rs17824989	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs17825013	0.85[CEU][hapmap]
rs34093317	1.00[ASN][1000 genomes]
rs55638557	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55654871	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55890195	0.84[EUR][1000 genomes]
rs55894137	0.84[EUR][1000 genomes]
rs55945889	0.84[EUR][1000 genomes]
rs56187356	0.84[EUR][1000 genomes]
rs56205628	0.87[EUR][1000 genomes]
rs56378908	0.87[EUR][1000 genomes]
rs60209369	0.80[EUR][1000 genomes]
rs7138353	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301153	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307383	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307676	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307874	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310715	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73304917	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74089125	1.00[ASN][1000 genomes]
rs74089155	0.84[EUR][1000 genomes]
rs74089159	0.95[EUR][1000 genomes]
rs74089163	0.95[EUR][1000 genomes]
rs9630296	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10506276	ZNF641	cis	Whole Blood	GTEx
rs10506276	LOC255411	cis	cerebellum	SCAN
rs10506276	NCKAP5L	cis	parietal	SCAN
rs10506276	ZNF641	cis	multi-tissue	Pritchard
rs10506276	DDN	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48592400-48594800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:48592600-48595200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr12:48592800-48594600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:48592800-48594600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr12:48592800-48594800	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr12:48592800-48595200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr12:48592800-48596000	Weak transcription	Gastric	stomach
8	chr12:48592800-48596000	Weak transcription	Ovary	ovary
9	chr12:48592800-48600400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:48593000-48594600	Enhancers	Fetal Intestine Large	intestine
11	chr12:48593000-48595000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:48593000-48595600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr12:48593000-48595600	Enhancers	Placenta	Placenta
14	chr12:48593000-48596600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:48593200-48594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:48593200-48595000	Enhancers	Adipose Nuclei	Adipose
17	chr12:48593200-48595000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:48593200-48595200	Enhancers	Psoas Muscle	Psoas
19	chr12:48593200-48596800	Weak transcription	Brain Substantia Nigra	brain
20	chr12:48593200-48599000	Weak transcription	Brain Angular Gyrus	brain
21	chr12:48593200-48600200	Weak transcription	Right Ventricle	heart
22	chr12:48593400-48594600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr12:48593400-48594600	Enhancers	Fetal Thymus	thymus
24	chr12:48593400-48596000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:48593400-48600800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:48593600-48595200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr12:48593600-48596600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:48593800-48594600	Enhancers	Right Atrium	heart
29	chr12:48593800-48594800	Enhancers	Rectal Smooth Muscle	rectum
30	chr12:48593800-48595200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:48593800-48596000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:48593800-48596000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:48593800-48596000	Weak transcription	Fetal Stomach	stomach
34	chr12:48593800-48596400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:48593800-48596600	Weak transcription	Left Ventricle	heart
36	chr12:48593800-48598400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:48593800-48598400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:48594000-48595000	Weak transcription	Small Intestine	intestine
39	chr12:48594000-48595200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr12:48594000-48595200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:48594000-48595200	Enhancers	Brain Anterior Caudate	brain
42	chr12:48594000-48595200	Enhancers	Fetal Lung	lung
43	chr12:48594000-48595600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:48594000-48595800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:48594000-48596800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr12:48594000-48598400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:48594200-48594600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:48594200-48594600	Enhancers	Lung	lung
49	chr12:48594200-48595000	Weak transcription	K562	blood
50	chr12:48594200-48595200	Enhancers	Primary hematopoietic stem cells	blood

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