Variant report

Variant	rs13246200
Chromosome Location	chr7:127540433-127540434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr7:127540140-127540876	SK-N-SH	brain:	n/a	n/a
2	GATA2	chr7:127540371-127540728	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr7:127540041-127540807	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr7:127540301-127540696	SH-SY5Y	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:127539859..127542368-chr7:127543054..127544559,2	K562	blood:
2	chr7:127535349..127538608-chr7:127539437..127541786,4	MCF-7	breast:
3	chr7:127530901..127533766-chr7:127540275..127542321,2	K562	blood:
4	chr7:127539496..127544017-chr7:127546415..127549727,4	MCF-7	breast:
5	chr7:127539523..127541289-chr7:127544674..127547671,2	K562	blood:

No data

Variant related genes	Relation type
SND1	TF binding region
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10487499	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487502	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155421	1.00[ASN][1000 genomes]
rs12375023	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531847	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532894	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534918	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540357	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706816	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706818	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706819	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12706820	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706822	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706823	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221709	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227201	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229973	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231367	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345283	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348103	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1362898	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468701	0.98[EUR][1000 genomes]
rs17151466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151639	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs17151653	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151668	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151682	1.00[ASN][1000 genomes]
rs17676654	1.00[ASN][1000 genomes]
rs1860934	0.80[AFR][1000 genomes]
rs325451	0.80[AFR][1000 genomes]
rs34026100	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688920	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34839191	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154268	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41464647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs55660321	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58406876	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58489175	1.00[ASN][1000 genomes]
rs6467157	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs67632185	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827668	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948605	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953231	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6959487	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232968	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232972	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234873	0.85[EUR][1000 genomes]
rs73234874	0.84[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[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7458839	0.99[EUR][1000 genomes]
rs7785596	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805021	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809182	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7810024	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894062	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917832	0.80[AFR][1000 genomes]
rs9649027	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649512	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13246200	SND1	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127505800-127542000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:127515400-127540600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr7:127526200-127544600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:127526600-127540600	Weak transcription	Fetal Brain Female	brain
5	chr7:127526600-127540600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr7:127528800-127569200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr7:127529000-127557200	Weak transcription	Esophagus	oesophagus
8	chr7:127529200-127540800	Weak transcription	Spleen	Spleen
9	chr7:127529200-127544600	Weak transcription	Thymus	Thymus
10	chr7:127529200-127545600	Weak transcription	Fetal Stomach	stomach
11	chr7:127529200-127546200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:127529200-127548400	Weak transcription	Right Ventricle	heart
13	chr7:127529200-127569400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr7:127529400-127542200	Weak transcription	Fetal Heart	heart
15	chr7:127529400-127551000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:127531800-127542000	Weak transcription	Fetal Kidney	kidney
17	chr7:127532200-127569200	Weak transcription	Hela-S3	cervix
18	chr7:127532400-127540600	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:127532400-127540600	Weak transcription	Gastric	stomach
20	chr7:127532400-127547400	Weak transcription	A549	lung
21	chr7:127532400-127569200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr7:127532600-127541000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:127532600-127541200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:127532600-127546000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr7:127532800-127540800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr7:127532800-127541000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr7:127532800-127541600	Weak transcription	Dnd41	blood
28	chr7:127532800-127544800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr7:127532800-127545600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:127533000-127540600	Weak transcription	Liver	Liver
31	chr7:127533000-127540800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:127533000-127541000	Weak transcription	Lung	lung
33	chr7:127533800-127541400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:127534000-127542200	Weak transcription	Adipose Nuclei	Adipose
35	chr7:127534400-127544400	Weak transcription	Fetal Brain Male	brain
36	chr7:127535000-127542600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr7:127535000-127543200	Enhancers	Fetal Intestine Large	intestine
38	chr7:127535800-127540800	Weak transcription	Ovary	ovary
39	chr7:127535800-127542800	Enhancers	Fetal Intestine Small	intestine
40	chr7:127536200-127540800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr7:127536200-127540800	Weak transcription	Left Ventricle	heart
42	chr7:127536600-127540800	Weak transcription	Fetal Thymus	thymus
43	chr7:127536800-127540600	Weak transcription	Primary T cells from cord blood	blood
44	chr7:127536800-127541200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr7:127537000-127540800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:127537000-127540800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr7:127537000-127541000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:127537600-127541600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr7:127537800-127541600	Weak transcription	Primary B cells from cord blood	blood
50	chr7:127538000-127542600	Enhancers	Cortex derived primary cultured neurospheres	brain

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