Variant report

Variant	rs3748143
Chromosome Location	chr8:8655237-8655238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10090152	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10093872	0.88[CEU][hapmap]
rs10100066	0.89[ASN][1000 genomes]
rs10103163	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10103282	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10110711	0.89[ASN][1000 genomes]
rs11774860	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11775486	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777812	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778326	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11778330	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11781430	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11906	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs11985640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17154743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17154756	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17154758	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17630714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17631022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17631052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048420	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2427	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs34722673	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35432123	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789857	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827810	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55657655	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55961293	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56100346	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73517985	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73519953	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7831224	0.84[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs964771	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs964772	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs964773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
2	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv1795023	chr8:8583943-8655580	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	esv1825234	chr8:8583943-8655580	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	esv1824870	chr8:8583943-8699382	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv610189	chr8:8590437-8664940	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv831228	chr8:8608387-8790790	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv1018828	chr8:8609880-8790660	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv1022331	chr8:8610035-8787981	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3748143	MFHAS1	cis	parietal	SCAN
rs3748143	TDH	cis	cerebellum	SCAN
rs3748143	MFHAS1	cis	cerebellum	SCAN
rs3748143	MAP7D2	trans	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8637600-8679800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:8640200-8655600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:8642800-8660000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr8:8644200-8655600	Weak transcription	Fetal Brain Male	brain
5	chr8:8646600-8658000	Weak transcription	Pancreas	Pancrea
6	chr8:8648600-8658000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr8:8649200-8657200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr8:8649200-8657200	Weak transcription	Colon Smooth Muscle	Colon
9	chr8:8649200-8657800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr8:8649200-8666400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:8649400-8657800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr8:8649400-8661800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:8649400-8663600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr8:8649400-8663800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr8:8649600-8657800	Weak transcription	Stomach Mucosa	stomach
16	chr8:8650600-8656000	Strong transcription	Dnd41	blood
17	chr8:8650800-8663400	Weak transcription	Hela-S3	cervix
18	chr8:8651000-8655400	Strong transcription	Fetal Intestine Small	intestine
19	chr8:8651200-8656200	Weak transcription	Esophagus	oesophagus
20	chr8:8651200-8657800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr8:8651600-8658000	Weak transcription	Aorta	Aorta
22	chr8:8651800-8657800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr8:8652400-8655400	Weak transcription	A549	lung
24	chr8:8652600-8659200	Weak transcription	Ovary	ovary
25	chr8:8653800-8655400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr8:8653800-8656800	Weak transcription	NHEK	skin
27	chr8:8653800-8657000	Weak transcription	Fetal Heart	heart
28	chr8:8653800-8657200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr8:8653800-8657200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr8:8653800-8657400	Weak transcription	Liver	Liver
31	chr8:8653800-8657400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr8:8653800-8657400	Weak transcription	Lung	lung
33	chr8:8653800-8657800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr8:8653800-8662000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr8:8653800-8662600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr8:8653800-8663400	Weak transcription	HMEC	breast
37	chr8:8653800-8674800	Weak transcription	Brain Germinal Matrix	brain
38	chr8:8654000-8657000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr8:8654000-8657200	Weak transcription	Gastric	stomach
40	chr8:8654000-8657600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr8:8654000-8657800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr8:8654000-8658000	Weak transcription	Fetal Intestine Large	intestine
43	chr8:8654000-8659400	Weak transcription	HepG2	liver
44	chr8:8654000-8663600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr8:8654000-8666800	Weak transcription	NHDF-Ad	bronchial
46	chr8:8654000-8666800	Weak transcription	NHLF	lung
47	chr8:8654000-8671000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr8:8654200-8658000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr8:8654600-8655400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr8:8654600-8655400	Flanking Active TSS	Primary B cells from cord blood	blood

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