Variant report

Variant	rs2492778
Chromosome Location	chr1:179299147-179299148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179294763..179296737-chr1:179297723..179299228,2	MCF-7	breast:
2	chr1:179049985..179051975-chr1:179298821..179301008,2	K562	blood:

Variant related genes	Relation type
ENSG00000186283	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1034269	0.81[CHB][hapmap]
rs10798655	0.84[ASN][1000 genomes]
rs10798656	0.81[CHB][hapmap]
rs10913714	0.81[CHB][hapmap]
rs10913718	0.81[CHB][hapmap]
rs12047131	0.81[CHB][hapmap]
rs12725375	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12749666	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1475799	0.81[CHB][hapmap]
rs1543876	0.88[GIH][hapmap]
rs17368880	0.81[CHB][hapmap]
rs2050450	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2050451	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2152318	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247061	0.94[ASN][1000 genomes]
rs2248979	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250352	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250477	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254214	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2254580	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs2254623	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255375	0.88[GIH][hapmap];0.83[LWK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs2257089	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2257100	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484440	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484443	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2484446	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492777	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493116	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2493117	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2493118	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2493119	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783391	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2783392	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2783393	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2902276	0.81[CHB][hapmap]
rs404818	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs433722	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4652364	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56371666	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824366	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425530	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6698438	0.81[CHB][hapmap]
rs6699698	0.81[CHB][hapmap]
rs7523431	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532172	0.81[CHB][hapmap]
rs7543894	0.81[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2492778	RASAL2	cis	parietal	SCAN
rs2492778	TDRD5	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179263800-179304600	Weak transcription	Lung	lung
2	chr1:179263800-179306400	Weak transcription	Gastric	stomach
3	chr1:179264600-179304600	Weak transcription	Right Ventricle	heart
4	chr1:179264600-179310200	Weak transcription	Brain Substantia Nigra	brain
5	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
6	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:179264800-179313800	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:179264800-179313800	Weak transcription	Fetal Brain Female	brain
9	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
11	chr1:179268400-179312000	Weak transcription	Fetal Thymus	thymus
12	chr1:179272600-179313800	Weak transcription	Brain Anterior Caudate	brain
13	chr1:179273000-179311600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:179274600-179302400	Weak transcription	Left Ventricle	heart
15	chr1:179274600-179304400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:179274600-179306000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:179275600-179311600	Weak transcription	HUVEC	blood vessel
18	chr1:179276400-179306200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:179276600-179304800	Weak transcription	Pancreas	Pancrea
20	chr1:179280400-179314000	Weak transcription	NHLF	lung
21	chr1:179281200-179300200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:179282000-179313000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:179282400-179304200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:179282400-179313800	Weak transcription	HSMMtube	muscle
25	chr1:179283200-179308600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:179286400-179313800	Weak transcription	Psoas Muscle	Psoas
27	chr1:179287400-179304400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:179289000-179299200	Weak transcription	Fetal Stomach	stomach
29	chr1:179290200-179300000	Strong transcription	Primary T cells from cord blood	blood
30	chr1:179290200-179300200	Strong transcription	Hela-S3	cervix
31	chr1:179290400-179310000	Weak transcription	Aorta	Aorta
32	chr1:179290600-179304200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:179290600-179308800	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:179290800-179314000	Weak transcription	NHEK	skin
35	chr1:179291000-179306000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:179291400-179304800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:179292000-179304800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:179292200-179307200	Weak transcription	Adipose Nuclei	Adipose
39	chr1:179292400-179299400	Strong transcription	Liver	Liver
40	chr1:179292400-179300000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:179292400-179328000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:179292600-179307400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:179293000-179304400	Weak transcription	Ovary	ovary
44	chr1:179293000-179311800	Weak transcription	Fetal Kidney	kidney
45	chr1:179293000-179322600	Weak transcription	Fetal Heart	heart
46	chr1:179293200-179304600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:179293600-179313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:179293800-179301800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:179293800-179311800	Weak transcription	HMEC	breast
50	chr1:179293800-179314000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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