Variant report

Variant	rs1410600
Chromosome Location	chr10:97070694-97070695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97049242..97050860-chr10:97068797..97070801,3	MCF-7	breast:
2	chr10:97063353..97065156-chr10:97068953..97071321,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107438	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11188298	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11596586	0.82[ASN][1000 genomes]
rs1360005	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1410597	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410598	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536557	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2274628	0.82[ASN][1000 genomes]
rs35204215	0.89[ASN][1000 genomes]
rs3740511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3814149	0.87[ASN][1000 genomes]
rs4917686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4918913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs61868664	0.89[ASN][1000 genomes]
rs6583996	0.87[ASN][1000 genomes]
rs7068295	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7068868	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7082473	0.82[ASN][1000 genomes]
rs7084585	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7084589	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7084645	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7897903	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7899506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7904853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7919271	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv552021	chr10:97053404-97071334	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1410600	AVPI1	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97055600-97072800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:97063400-97072400	Weak transcription	Fetal Brain Female	brain
3	chr10:97063400-97073600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:97064000-97073200	Weak transcription	Fetal Muscle Leg	muscle
5	chr10:97064600-97078200	Weak transcription	Colonic Mucosa	Colon
6	chr10:97066000-97073000	Weak transcription	Fetal Intestine Large	intestine
7	chr10:97066000-97073600	Weak transcription	Fetal Intestine Small	intestine
8	chr10:97067000-97070800	Enhancers	Stomach Mucosa	stomach
9	chr10:97067200-97073400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr10:97067600-97070800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr10:97067600-97071200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr10:97067800-97071000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr10:97068200-97071000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr10:97068400-97071000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr10:97068400-97072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:97068600-97071000	Enhancers	Primary B cells from peripheral blood	blood
17	chr10:97068600-97072000	Weak transcription	Adipose Nuclei	Adipose
18	chr10:97068600-97072800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:97068600-97073800	Weak transcription	Brain Angular Gyrus	brain
20	chr10:97069000-97070800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr10:97069000-97072400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:97069000-97073000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:97069000-97073200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr10:97069000-97073400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr10:97069000-97073600	Weak transcription	HepG2	liver
26	chr10:97069000-97075600	Enhancers	K562	blood
27	chr10:97069200-97072200	Weak transcription	HUVEC	blood vessel
28	chr10:97069200-97072600	Weak transcription	Psoas Muscle	Psoas
29	chr10:97069200-97072600	Weak transcription	HSMMtube	muscle
30	chr10:97069200-97087000	Weak transcription	HSMM	muscle
31	chr10:97069400-97072400	Weak transcription	Left Ventricle	heart
32	chr10:97069400-97072600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:97069400-97074000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr10:97069600-97072000	Weak transcription	Hela-S3	cervix
35	chr10:97069600-97073000	Weak transcription	Fetal Stomach	stomach
36	chr10:97069600-97073800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:97069800-97070800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr10:97069800-97071000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr10:97069800-97072200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr10:97069800-97075200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr10:97070000-97071000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr10:97070000-97071000	Enhancers	Gastric	stomach
43	chr10:97070000-97071200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr10:97070000-97073000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:97070200-97070800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr10:97070200-97070800	Enhancers	Small Intestine	intestine
47	chr10:97070200-97071000	Genic enhancers	Aorta	Aorta
48	chr10:97070200-97071000	Enhancers	Esophagus	oesophagus
49	chr10:97070200-97071000	Enhancers	Spleen	Spleen
50	chr10:97070200-97071200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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