Variant report

Variant	rs12540357
Chromosome Location	chr7:127390649-127390650
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127388845..127391167-chr7:127400870..127402708,2	K562	blood:
2	chr7:127389289..127393193-chr7:127394963..127397566,4	K562	blood:
3	chr7:127390567..127392774-chr7:127400064..127401967,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10487499	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487502	1.00[ASN][1000 genomes]
rs12154492	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375023	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531847	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532894	1.00[ASN][1000 genomes]
rs12534918	1.00[ASN][1000 genomes]
rs12706816	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706818	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706819	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12706820	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706821	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706822	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706823	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221709	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227201	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229973	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231367	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236338	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238924	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246200	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246286	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345283	1.00[ASN][1000 genomes]
rs1348103	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419970	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468701	0.84[EUR][1000 genomes]
rs17151466	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151488	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151507	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151653	1.00[ASN][1000 genomes]
rs17676654	1.00[ASN][1000 genomes]
rs327508	1.00[ASN][1000 genomes]
rs34026100	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688920	1.00[ASN][1000 genomes]
rs34839191	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154268	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35660964	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55660321	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58406876	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67632185	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827668	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948605	1.00[ASN][1000 genomes]
rs6959487	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232968	1.00[ASN][1000 genomes]
rs73232972	1.00[ASN][1000 genomes]
rs73234873	0.85[EUR][1000 genomes]
rs73234874	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741094	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7458839	0.85[EUR][1000 genomes]
rs7785596	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809182	0.85[EUR][1000 genomes]
rs7810024	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894062	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649027	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649512	0.82[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	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats 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	21 gene(s)	inside rSNPs	diseases
5	nsv1030387	chr7:127348973-127455890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12540357	SND1	cis	Artery Tibial	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127361200-127391400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:127362600-127400000	Weak transcription	Small Intestine	intestine
3	chr7:127363400-127391000	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:127363400-127391400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:127366000-127391000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:127366200-127391200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:127368800-127391600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:127370000-127391200	Weak transcription	NHDF-Ad	bronchial
9	chr7:127371200-127391600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:127371800-127391200	Weak transcription	Esophagus	oesophagus
11	chr7:127372000-127391000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:127372200-127391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:127372200-127395600	Weak transcription	Thymus	Thymus
14	chr7:127372400-127391200	Weak transcription	Brain Anterior Caudate	brain
15	chr7:127372400-127391200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:127372600-127391000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:127372600-127391200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:127372600-127394600	Weak transcription	Ovary	ovary
19	chr7:127373200-127391200	Weak transcription	Brain Substantia Nigra	brain
20	chr7:127373200-127410000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr7:127373400-127391000	Weak transcription	HSMMtube	muscle
22	chr7:127374000-127391000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:127374800-127392200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:127375200-127391200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr7:127375200-127395800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:127375400-127391200	Weak transcription	Adipose Nuclei	Adipose
27	chr7:127375400-127391800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:127375400-127417400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr7:127375600-127401000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:127376800-127409200	Weak transcription	HUVEC	blood vessel
31	chr7:127377000-127409200	Weak transcription	NHLF	lung
32	chr7:127377200-127391200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:127377400-127390800	Weak transcription	Osteobl	bone
34	chr7:127377400-127391000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:127377400-127391200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:127377400-127391200	Weak transcription	Lung	lung
37	chr7:127377800-127390800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:127378000-127391200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:127378200-127412200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr7:127378400-127391200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr7:127378800-127401200	Weak transcription	Placenta	Placenta
42	chr7:127379000-127391200	Weak transcription	Fetal Muscle Leg	muscle
43	chr7:127379200-127391000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:127379200-127391200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr7:127379200-127437400	Weak transcription	Fetal Stomach	stomach
46	chr7:127379400-127391200	Weak transcription	Left Ventricle	heart
47	chr7:127380000-127409200	Weak transcription	Aorta	Aorta
48	chr7:127380200-127391400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:127380600-127391000	Weak transcription	NH-A	brain
50	chr7:127380800-127391200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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