Variant report

Variant	rs12706821
Chromosome Location	chr7:127521693-127521694
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127519364..127522726-chr7:127524466..127527535,4	K562	blood:
2	chr7:127501679..127503363-chr7:127520843..127522345,2	MCF-7	breast:
3	chr7:127514549..127522691-chr7:127524662..127530854,11	K562	blood:

Variant related genes	Relation type
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10487499	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487502	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155421	1.00[ASN][1000 genomes]
rs12375023	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531847	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532894	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534918	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540357	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706816	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706818	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706819	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12706820	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706822	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706823	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221709	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227201	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231367	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345283	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348103	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1362898	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468701	0.99[EUR][1000 genomes]
rs17151466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151639	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs17151653	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151668	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151682	1.00[ASN][1000 genomes]
rs17151707	1.00[GIH][hapmap];0.86[MEX][hapmap]
rs17676654	1.00[ASN][1000 genomes]
rs327508	1.00[ASN][1000 genomes]
rs34026100	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688920	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34839191	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154268	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35660964	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779529	0.91[AFR][1000 genomes]
rs41464647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap]
rs55660321	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58406876	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58489175	1.00[ASN][1000 genomes]
rs6467157	1.00[CHB][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs67632185	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827668	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948605	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953231	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs6959487	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962635	1.00[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs73232968	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232972	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234873	0.86[EUR][1000 genomes]
rs73234874	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238078	1.00[ASN][1000 genomes]
rs741094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741599	0.85[ASW][hapmap];0.83[YRI][hapmap]
rs7458839	0.99[EUR][1000 genomes]
rs7785596	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805021	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809182	1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes]
rs7810024	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894062	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649027	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649512	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12706821	SND1	cis	Artery Tibial	GTEx
rs12706821	ARF5	cis	cerebellum	SCAN
rs12706821	HYAL4	cis	cerebellum	SCAN
rs12706821	GPR37	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127485200-127527800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:127485600-127522000	Weak transcription	Placenta	Placenta
3	chr7:127491400-127527800	Weak transcription	Liver	Liver
4	chr7:127498600-127525000	Weak transcription	Fetal Intestine Small	intestine
5	chr7:127498800-127521800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:127498800-127524600	Weak transcription	Gastric	stomach
7	chr7:127498800-127525600	Weak transcription	Fetal Stomach	stomach
8	chr7:127500200-127521800	Weak transcription	Pancreas	Pancrea
9	chr7:127500200-127535400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:127500400-127527800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr7:127500400-127527800	Weak transcription	Dnd41	blood
12	chr7:127500400-127528000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:127500600-127527400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:127501000-127527800	Weak transcription	Fetal Thymus	thymus
15	chr7:127503000-127524400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:127504600-127522000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr7:127505400-127537800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr7:127505600-127525200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:127505600-127528400	Weak transcription	Hela-S3	cervix
20	chr7:127505800-127539600	Weak transcription	Small Intestine	intestine
21	chr7:127505800-127542000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:127507000-127525000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:127507400-127524600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:127509400-127521800	Weak transcription	Left Ventricle	heart
25	chr7:127509400-127521800	Weak transcription	Right Atrium	heart
26	chr7:127512200-127525000	Weak transcription	Fetal Heart	heart
27	chr7:127512600-127528000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr7:127514200-127521800	Weak transcription	Brain Angular Gyrus	brain
29	chr7:127514200-127521800	Weak transcription	Psoas Muscle	Psoas
30	chr7:127514200-127522000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:127514400-127524600	Weak transcription	HepG2	liver
32	chr7:127514800-127531000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr7:127515400-127527800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:127515400-127540600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr7:127516000-127522600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:127516000-127527000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:127516000-127527800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:127516000-127528000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:127516200-127525000	Weak transcription	Primary T cells from cord blood	blood
40	chr7:127516400-127525400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:127516400-127528600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr7:127516400-127540200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr7:127516600-127522200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr7:127516600-127524400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:127516600-127524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:127516600-127524400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:127516600-127524400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:127516600-127524400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr7:127516600-127524400	Weak transcription	GM12878-XiMat	blood
50	chr7:127516800-127524400	Weak transcription	NHEK	skin

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