Variant report

Variant	rs1510278
Chromosome Location	chr3:156257121-156257122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156255091..156257756-chr3:156296405..156299057,2	K562	blood:
2	chr3:156254995..156257951-chr3:156406375..156408006,2	K562	blood:
3	chr3:156254209..156257185-chr3:156353690..156355204,2	K562	blood:
4	chr3:156256280..156259160-chr3:156390953..156393819,2	MCF-7	breast:
5	chr3:156165868..156167744-chr3:156256177..156258339,2	K562	blood:
6	chr3:156256323..156258307-chr3:156531885..156534419,2	MCF-7	breast:
7	chr3:156254673..156257232-chr3:156395894..156398875,3	K562	blood:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1027915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs10513493	0.94[CEU][hapmap]
rs1129109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510277	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680280	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680282	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6785996	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6797292	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs907060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908807	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9820091	0.94[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs9856073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv877683	chr3:156180366-156272351	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1510278	SSR3	Cis_1M	lymphoblastoid	RTeQTL
rs1510278	C3orf33	cis	cerebellum	SCAN
rs1510278	KCNAB1	Cis_1M	lymphoblastoid	RTeQTL
rs1510278	LXN	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156240400-156260200	Weak transcription	Esophagus	oesophagus
2	chr3:156243200-156258800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:156245400-156257200	Weak transcription	Fetal Brain Male	brain
4	chr3:156246800-156263600	Weak transcription	Fetal Brain Female	brain
5	chr3:156247200-156263800	Weak transcription	Thymus	Thymus
6	chr3:156247600-156257200	Weak transcription	Hela-S3	cervix
7	chr3:156249000-156264600	Weak transcription	Brain Germinal Matrix	brain
8	chr3:156251600-156259200	Weak transcription	Ovary	ovary
9	chr3:156252000-156263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:156252000-156270200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:156252200-156268600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:156253000-156259200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:156253400-156257400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:156253400-156260800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:156253400-156268200	Weak transcription	Gastric	stomach
16	chr3:156253600-156260200	Weak transcription	Fetal Stomach	stomach
17	chr3:156253600-156268200	Weak transcription	Small Intestine	intestine
18	chr3:156253600-156271400	Weak transcription	Stomach Mucosa	stomach
19	chr3:156253800-156257400	Weak transcription	Fetal Kidney	kidney
20	chr3:156253800-156258600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:156253800-156258800	Weak transcription	Brain Substantia Nigra	brain
22	chr3:156253800-156259400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:156253800-156259800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:156253800-156260000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:156253800-156260000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:156253800-156260800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:156253800-156260800	Weak transcription	Right Ventricle	heart
28	chr3:156253800-156261200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:156253800-156261400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:156253800-156270800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:156254000-156258600	Weak transcription	Brain Angular Gyrus	brain
32	chr3:156254000-156259400	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:156254000-156259800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:156254000-156260000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:156254000-156260000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:156254200-156270200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr3:156254600-156259000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:156254600-156259200	Weak transcription	Placenta	Placenta
39	chr3:156254600-156260200	Weak transcription	Fetal Heart	heart
40	chr3:156254600-156265400	Strong transcription	Liver	Liver
41	chr3:156255200-156257800	Genic enhancers	HSMM	muscle
42	chr3:156255200-156268600	Strong transcription	Dnd41	blood
43	chr3:156255200-156270600	Strong transcription	A549	lung
44	chr3:156255600-156257600	Enhancers	Colon Smooth Muscle	Colon
45	chr3:156255600-156257800	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr3:156255600-156258000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:156255600-156259600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:156255600-156259800	Strong transcription	HUVEC	blood vessel
49	chr3:156255600-156261200	Strong transcription	NHDF-Ad	bronchial
50	chr3:156255600-156261400	Strong transcription	Osteobl	bone

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