Variant report

Variant	rs3780000
Chromosome Location	chr8:59756898-59756899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10090233	0.97[EUR][1000 genomes]
rs10099884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10103680	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12542489	0.80[YRI][hapmap]
rs13251536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13262120	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs1349115	0.81[YRI][hapmap]
rs16924032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16924069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16924102	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16924122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34855090	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35553018	0.81[EUR][1000 genomes]
rs3779998	0.90[CEU][hapmap]
rs6471754	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72649459	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7813495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7817609	0.81[CEU][hapmap]
rs7821556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][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	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3780000	IMPAD1	cis	cerebellum	SCAN
rs3780000	CHCHD7	cis	cerebellum	SCAN
rs3780000	LYN	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59715200-59757400	Weak transcription	Fetal Intestine Large	intestine
2	chr8:59720800-59762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:59722400-59757200	Strong transcription	Dnd41	blood
4	chr8:59730800-59770800	Strong transcription	Fetal Thymus	thymus
5	chr8:59745600-59770800	Weak transcription	Fetal Kidney	kidney
6	chr8:59745800-59770800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:59746400-59773200	Weak transcription	Fetal Intestine Small	intestine
8	chr8:59746600-59763600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr8:59746800-59763600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr8:59747000-59757600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:59747400-59757800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr8:59747400-59760400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:59747400-59770800	Weak transcription	Pancreas	Pancrea
14	chr8:59749200-59757600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr8:59749200-59762600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr8:59750800-59757600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr8:59750800-59760000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr8:59750800-59761800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr8:59750800-59762600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr8:59750800-59771000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr8:59751000-59761600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:59751000-59763400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr8:59752400-59757600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr8:59753600-59762600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr8:59753800-59758800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr8:59754000-59762600	Weak transcription	Thymus	Thymus
27	chr8:59755000-59762600	Weak transcription	NHLF	lung
28	chr8:59755200-59759200	Weak transcription	HSMM	muscle
29	chr8:59755400-59757200	Strong transcription	Primary hematopoietic stem cells	blood
30	chr8:59755400-59757200	Weak transcription	HUVEC	blood vessel
31	chr8:59755400-59757400	Weak transcription	Osteobl	bone
32	chr8:59755400-59757600	Weak transcription	NHDF-Ad	bronchial
33	chr8:59755400-59759200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr8:59755400-59759800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr8:59755400-59762600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr8:59755400-59762800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr8:59755400-59762800	Weak transcription	Gastric	stomach
38	chr8:59755600-59757400	Weak transcription	NH-A	brain
39	chr8:59755600-59757600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr8:59755600-59759200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr8:59755600-59759200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr8:59755600-59759200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr8:59755600-59759800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr8:59755600-59762400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr8:59755600-59770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr8:59755800-59757400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr8:59755800-59757600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr8:59755800-59757600	Weak transcription	NHEK	skin
49	chr8:59755800-59759600	Enhancers	Fetal Lung	lung
50	chr8:59755800-59772200	Weak transcription	Small Intestine	intestine

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