Variant report

Variant	rs11249992
Chromosome Location	chr8:10220412-10220413
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11249995	0.80[CEU][hapmap]
rs11249996	0.80[CEU][hapmap]
rs11249999	0.80[CEU][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11250001	0.85[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs11250002	0.84[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11779205	0.84[CEU][hapmap]
rs11989640	0.80[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12541491	0.84[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs12543645	0.84[CEU][hapmap];0.88[GIH][hapmap]
rs12547997	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs13254942	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs13264580	0.85[ASN][1000 genomes]
rs13273009	0.81[CHD][hapmap]
rs1986677	0.86[CHD][hapmap]
rs1986972	0.84[CEU][hapmap];0.81[GIH][hapmap]
rs2001337	0.84[CEU][hapmap];0.85[ASN][1000 genomes]
rs2001338	0.80[CEU][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.80[MKK][hapmap];0.85[ASN][1000 genomes]
rs3088186	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.91[ASN][1000 genomes]
rs34381075	0.90[ASN][1000 genomes]
rs34487437	0.90[ASN][1000 genomes]
rs4240645	0.87[CEU][hapmap]
rs4292737	0.84[CEU][hapmap]
rs6601447	0.85[CHD][hapmap]
rs7460436	0.87[CEU][hapmap]
rs7842443	0.85[CHD][hapmap]
rs9650650	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1016347	chr8:10091475-10223667	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv890347	chr8:10153082-10331636	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv527326	chr8:10199548-10320019	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1018940	chr8:10200886-10220973	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11249992	MFHAS1	cis	cerebellum	SCAN
rs11249992	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs11249992	RP1L1	cis	cerebellum	SCAN
rs11249992	FLJ10661	cis	parietal	SCAN
rs11249992	DEFB136	cis	parietal	SCAN
rs11249992	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs11249992	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10192600-10282400	Weak transcription	Gastric	stomach
2	chr8:10193000-10235000	Weak transcription	Pancreas	Pancrea
3	chr8:10196800-10228000	Weak transcription	Liver	Liver
4	chr8:10201800-10221800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:10204400-10221800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr8:10206200-10222800	Weak transcription	Aorta	Aorta
7	chr8:10209400-10220600	Weak transcription	Brain Angular Gyrus	brain
8	chr8:10216200-10220600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:10217400-10220600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:10217400-10220600	Weak transcription	Right Ventricle	heart
11	chr8:10217600-10226400	Enhancers	Fetal Brain Male	brain
12	chr8:10217800-10220600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:10218200-10220800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr8:10218400-10221000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr8:10218600-10222800	Weak transcription	Brain Anterior Caudate	brain
16	chr8:10218800-10222000	Weak transcription	NHDF-Ad	bronchial
17	chr8:10218800-10223200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr8:10218800-10223400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr8:10219200-10220600	Weak transcription	HMEC	breast
20	chr8:10219400-10221000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr8:10219400-10222000	Enhancers	Spleen	Spleen
22	chr8:10219400-10224600	Enhancers	Fetal Muscle Leg	muscle
23	chr8:10219600-10220600	Enhancers	Primary hematopoietic stem cells	blood
24	chr8:10219600-10221000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr8:10219800-10220600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr8:10219800-10220800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:10219800-10221200	Enhancers	Stomach Smooth Muscle	stomach
28	chr8:10219800-10221400	Enhancers	NHEK	skin
29	chr8:10219800-10222200	Enhancers	Primary T cells from cord blood	blood
30	chr8:10219800-10223200	Enhancers	Fetal Brain Female	brain
31	chr8:10220000-10220600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr8:10220000-10220800	Enhancers	Fetal Stomach	stomach
33	chr8:10220000-10221000	Enhancers	Fetal Muscle Trunk	muscle
34	chr8:10220000-10221000	Enhancers	Fetal Thymus	thymus
35	chr8:10220000-10221000	Enhancers	Lung	lung
36	chr8:10220000-10221200	Enhancers	Brain Germinal Matrix	brain
37	chr8:10220000-10221400	Enhancers	Fetal Lung	lung
38	chr8:10220000-10221400	Enhancers	Right Atrium	heart
39	chr8:10220000-10222600	Enhancers	Left Ventricle	heart
40	chr8:10220000-10224400	Enhancers	Placenta Amnion	Placenta Amnion
41	chr8:10220200-10220600	Enhancers	H1 Cell Line	embryonic stem cell
42	chr8:10220200-10220600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr8:10220200-10220600	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr8:10220200-10220800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr8:10220200-10220800	Enhancers	Duodenum Mucosa	Duodenum
46	chr8:10220200-10220800	Enhancers	HUVEC	blood vessel
47	chr8:10220200-10221000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr8:10220200-10221000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr8:10220200-10221200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr8:10220200-10221200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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