Variant report

Variant	rs1409708
Chromosome Location	chr10:97296291-97296292
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:97289605..97292487-chr10:97295547..97298455,3	K562	blood:
2	chr10:97293527..97296505-chr10:97299046..97301710,3	K562	blood:
3	chr10:97292805..97294377-chr10:97295595..97297617,2	K562	blood:
4	chr10:97290800..97293543-chr10:97293667..97298455,5	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10736089	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1326931	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1326933	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1326935	1.00[CHD][hapmap]
rs1326937	1.00[JPT][hapmap]
rs1326938	1.00[JPT][hapmap]
rs1326939	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1359723	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1359724	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1409715	1.00[JPT][hapmap]
rs1536441	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1536447	1.00[CHD][hapmap]
rs1571132	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1609588	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1819287	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2031683	1.00[JPT][hapmap]
rs3927490	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4457684	1.00[JPT][hapmap]
rs4466758	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4498913	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4592368	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4638246	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4918942	1.00[JPT][hapmap]
rs4918945	1.00[JPT][hapmap]
rs4918946	1.00[JPT][hapmap]
rs6584005	1.00[JPT][hapmap]
rs6584006	1.00[CHD][hapmap];0.80[EUR][1000 genomes]
rs6584008	1.00[JPT][hapmap]
rs7904778	0.81[EUR][1000 genomes]
rs7910345	0.80[EUR][1000 genomes]
rs7912249	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7921696	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7924227	1.00[JPT][hapmap]
rs943339	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs943340	1.00[JPT][hapmap]
rs943348	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1808679	chr10:97266478-97316855	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1409708	TM9SF3	cis	parietal	SCAN
rs1409708	IDE	cis	cerebellum	SCAN
rs1409708	CRTAC1	cis	cerebellum	SCAN
rs1409708	AVPI1	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97280800-97301400	Enhancers	Fetal Heart	heart
2	chr10:97281600-97296400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:97282200-97304400	Weak transcription	Brain Germinal Matrix	brain
4	chr10:97283200-97296400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:97289200-97299200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr10:97289200-97309000	Enhancers	Left Ventricle	heart
7	chr10:97289400-97303800	Weak transcription	HSMM	muscle
8	chr10:97290000-97298600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr10:97290000-97301400	Enhancers	Rectal Smooth Muscle	rectum
10	chr10:97290400-97298800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr10:97290600-97301800	Weak transcription	Ovary	ovary
12	chr10:97291200-97297200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr10:97291200-97301000	Weak transcription	Fetal Brain Female	brain
14	chr10:97291800-97296600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:97291800-97308600	Enhancers	Colon Smooth Muscle	Colon
16	chr10:97292000-97298400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr10:97292200-97299600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:97292400-97298600	Enhancers	K562	blood
19	chr10:97292600-97299800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:97292600-97299800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr10:97292600-97300600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr10:97293000-97297400	Weak transcription	Pancreas	Pancrea
23	chr10:97293000-97298800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr10:97293000-97299600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:97293000-97299800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr10:97293000-97300400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr10:97293200-97297400	Enhancers	Fetal Stomach	stomach
28	chr10:97293200-97302800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr10:97293400-97305400	Enhancers	Right Atrium	heart
30	chr10:97293400-97306000	Enhancers	Fetal Intestine Large	intestine
31	chr10:97293600-97296400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr10:97293600-97299800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr10:97293600-97302000	Weak transcription	Adipose Nuclei	Adipose
34	chr10:97293800-97296600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr10:97294200-97297600	Enhancers	Brain Cingulate Gyrus	brain
36	chr10:97294400-97299200	Enhancers	Fetal Lung	lung
37	chr10:97294600-97298400	Enhancers	Brain Anterior Caudate	brain
38	chr10:97294800-97296400	Enhancers	Fetal Intestine Small	intestine
39	chr10:97294800-97296400	Weak transcription	Lung	lung
40	chr10:97294800-97297600	Enhancers	Brain Substantia Nigra	brain
41	chr10:97295000-97296400	Weak transcription	Gastric	stomach
42	chr10:97295000-97296400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr10:97295000-97296400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr10:97295000-97296400	Weak transcription	Spleen	Spleen
45	chr10:97295000-97297400	Weak transcription	Psoas Muscle	Psoas
46	chr10:97295000-97299400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr10:97295000-97305200	Enhancers	Stomach Mucosa	stomach
48	chr10:97295400-97297600	Enhancers	HUVEC	blood vessel
49	chr10:97295600-97297000	Enhancers	Fetal Kidney	kidney
50	chr10:97295600-97297000	Enhancers	Fetal Muscle Leg	muscle

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