Variant report

Variant	rs10798656
Chromosome Location	chr1:179264291-179264292
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1034269	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798659	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913713	0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12024910	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12047131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12749666	0.81[CHB][hapmap]
rs1475799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17368880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1964175	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2152318	0.81[CHB][hapmap]
rs2250477	0.81[CHB][hapmap]
rs2492778	0.81[CHB][hapmap]
rs2493119	0.81[CHB][hapmap]
rs2493121	0.90[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2783391	0.81[CHB][hapmap]
rs2783393	0.81[CHB][hapmap]
rs2862616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2902276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2902277	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3923881	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3923882	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4278336	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4446926	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4651022	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425524	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425526	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425533	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6662229	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6667804	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6671532	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6680899	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6681505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685245	0.81[EUR][1000 genomes]
rs6691771	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6694235	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6696464	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6696781	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698438	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699698	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6704240	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7354893	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522641	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7532172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7543894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9803742	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10798656	ABL2	cis	parietal	SCAN
rs10798656	TOR3A	cis	cerebellum	SCAN
rs10798656	TDRD5	cis	parietal	SCAN
rs10798656	RASAL2	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179261800-179265800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:179262200-179264400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:179262200-179264400	Active TSS	HSMM	muscle
4	chr1:179262200-179264800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:179262400-179264400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:179262400-179264400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:179262400-179264400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:179262400-179264400	Active TSS	Left Ventricle	heart
9	chr1:179262400-179264400	Active TSS	Ovary	ovary
10	chr1:179262400-179264600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:179262400-179264600	Active TSS	Brain Germinal Matrix	brain
12	chr1:179262400-179264600	Active TSS	Pancreas	Pancrea
13	chr1:179262400-179264600	Active TSS	Psoas Muscle	Psoas
14	chr1:179262400-179264800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr1:179262400-179264800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:179262600-179264400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:179262600-179264400	Active TSS	Brain Anterior Caudate	brain
18	chr1:179262600-179264400	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr1:179262600-179264600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:179262800-179264400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:179262800-179264600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:179262800-179264800	Active TSS	NHLF	lung
23	chr1:179263400-179264600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:179263400-179264800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:179263600-179264400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr1:179263600-179264400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:179263600-179264600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr1:179263600-179264800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:179263600-179264800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr1:179263600-179264800	Enhancers	Fetal Heart	heart
31	chr1:179263600-179266600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:179263800-179264400	Enhancers	Fetal Thymus	thymus
33	chr1:179263800-179264600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:179263800-179264600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr1:179263800-179264600	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr1:179263800-179264800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:179263800-179264800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr1:179263800-179264800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr1:179263800-179264800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr1:179263800-179264800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:179263800-179265000	Flanking Active TSS	Dnd41	blood
42	chr1:179263800-179267600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:179263800-179268400	Enhancers	Primary B cells from peripheral blood	blood
44	chr1:179263800-179304600	Weak transcription	Lung	lung
45	chr1:179263800-179306400	Weak transcription	Gastric	stomach
46	chr1:179264000-179264400	Flanking Active TSS	Liver	Liver
47	chr1:179264000-179264400	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr1:179264000-179264400	Flanking Active TSS	Fetal Lung	lung
49	chr1:179264000-179264400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:179264000-179264400	Flanking Active TSS	Stomach Smooth Muscle	stomach

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