Variant report

Variant	rs12411861
Chromosome Location	chr10:97299366-97299367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:97299249..97301273-chr10:97310241..97312398,2	K562	blood:
2	chr10:97284547..97287564-chr10:97299273..97302569,3	K562	blood:
3	chr10:97293527..97296505-chr10:97299046..97301710,3	K562	blood:
4	chr10:97298258..97302790-chr10:97302901..97306757,8	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10786218	0.82[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs10882614	0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882615	0.85[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882616	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882617	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882618	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188355	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188357	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188359	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12219483	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12416299	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs17458865	1.00[CEU][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes]
rs17537576	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs55873943	0.95[EUR][1000 genomes]
rs56353860	0.99[EUR][1000 genomes]
rs61869973	0.86[EUR][1000 genomes]
rs61869974	0.86[EUR][1000 genomes]
rs61869975	0.85[EUR][1000 genomes]
rs61869976	0.87[EUR][1000 genomes]
rs61870045	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61870046	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61870048	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61870049	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61870050	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61870051	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61870052	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7069574	1.00[JPT][hapmap]
rs7085647	0.82[CEU][hapmap];0.86[EUR][1000 genomes]

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
rs12411861	CYP26A1	cis	cerebellum	SCAN
rs12411861	CYP2C8	cis	parietal	SCAN
rs12411861	CPEB3	cis	cerebellum	SCAN
rs12411861	C10orf62	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97280800-97301400	Enhancers	Fetal Heart	heart
2	chr10:97282200-97304400	Weak transcription	Brain Germinal Matrix	brain
3	chr10:97289200-97309000	Enhancers	Left Ventricle	heart
4	chr10:97289400-97303800	Weak transcription	HSMM	muscle
5	chr10:97290000-97301400	Enhancers	Rectal Smooth Muscle	rectum
6	chr10:97290600-97301800	Weak transcription	Ovary	ovary
7	chr10:97291200-97301000	Weak transcription	Fetal Brain Female	brain
8	chr10:97291800-97308600	Enhancers	Colon Smooth Muscle	Colon
9	chr10:97292200-97299600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:97292600-97299800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:97292600-97299800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:97292600-97300600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr10:97293000-97299600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr10:97293000-97299800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr10:97293000-97300400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:97293200-97302800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr10:97293400-97305400	Enhancers	Right Atrium	heart
18	chr10:97293400-97306000	Enhancers	Fetal Intestine Large	intestine
19	chr10:97293600-97299800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr10:97293600-97302000	Weak transcription	Adipose Nuclei	Adipose
21	chr10:97295000-97299400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr10:97295000-97305200	Enhancers	Stomach Mucosa	stomach
23	chr10:97296000-97299800	Weak transcription	Small Intestine	intestine
24	chr10:97296200-97299400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr10:97296200-97301400	Weak transcription	Colonic Mucosa	Colon
26	chr10:97296200-97306400	Enhancers	Liver	Liver
27	chr10:97296400-97302400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr10:97296400-97311400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr10:97296600-97299400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr10:97296600-97302800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:97296800-97312600	Weak transcription	Placenta	Placenta
32	chr10:97297000-97302600	Weak transcription	HSMMtube	muscle
33	chr10:97297200-97299800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:97297200-97300400	Weak transcription	Spleen	Spleen
35	chr10:97297200-97301400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr10:97297200-97302800	Weak transcription	Fetal Brain Male	brain
37	chr10:97297400-97299600	Weak transcription	Brain Angular Gyrus	brain
38	chr10:97297600-97299600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr10:97297600-97300200	Genic enhancers	Aorta	Aorta
40	chr10:97298200-97299800	Weak transcription	Psoas Muscle	Psoas
41	chr10:97298200-97301400	Weak transcription	Esophagus	oesophagus
42	chr10:97298200-97302000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr10:97298200-97305000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:97298200-97308200	Enhancers	Fetal Muscle Leg	muscle
45	chr10:97298400-97299400	Weak transcription	Right Ventricle	heart
46	chr10:97298400-97300600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr10:97298400-97300600	Weak transcription	Gastric	stomach
48	chr10:97298400-97300600	Weak transcription	Lung	lung
49	chr10:97298400-97300800	Enhancers	Fetal Intestine Small	intestine
50	chr10:97298400-97305200	Enhancers	Duodenum Smooth Muscle	Duodenum

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