Variant report

Variant	rs2304576
Chromosome Location	chr3:53922257-53922258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53921644..53923214-chr3:53923445..53925751,2	MCF-7	breast:
2	chr3:53914370..53917222-chr3:53919581..53923156,3	MCF-7	breast:
3	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
4	chr3:53919776..53924259-chr3:53924368..53927481,7	K562	blood:
5	chr3:53914339..53916278-chr3:53921868..53924184,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACTR8-2	chr3:53922023-53922510	NONHSAT090008

Variant related genes	Relation type
ENSG00000222888	Chromatin interaction
ENSG00000113811	Chromatin interaction
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1020082	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1134091	0.90[EUR][1000 genomes]
rs12632292	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17053568	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17053590	1.00[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs1982171	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2241806	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276840	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs2276843	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276844	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276845	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2289203	1.00[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs2304575	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2884631	0.87[EUR][1000 genomes]
rs3017	0.81[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs3733075	0.84[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs3733079	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3733083	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3821868	0.86[EUR][1000 genomes]
rs3821869	0.84[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs41292476	0.88[EUR][1000 genomes]
rs4141606	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45511795	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4687594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687753	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs4687756	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4687758	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687760	0.87[EUR][1000 genomes]
rs55917919	0.93[EUR][1000 genomes]
rs56743403	0.92[EUR][1000 genomes]
rs57398949	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62253003	0.81[EUR][1000 genomes]
rs62253004	0.81[EUR][1000 genomes]
rs6445612	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs709324	0.87[EUR][1000 genomes]
rs73078007	0.84[EUR][1000 genomes]
rs9840445	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9849951	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9850063	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9860367	0.87[EUR][1000 genomes]
rs9880056	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs999515	0.96[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2304576	IL17RB	cis	parietal	SCAN
rs2304576	ACTR8	cis	parietal	SCAN
rs2304576	ACTR8	cis	lymphoblastoid	seeQTL
rs2304576	SFMBT1	cis	cerebellum	SCAN
rs2304576	IL17RB	cis	cerebellum	SCAN
rs2304576	ACTR8	cis	Thyroid	GTEx
rs2304576	ACTR8	cis	cerebellum	SCAN
rs2304576	PHF7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53916200-53924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:53916200-53924800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53916600-53923400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:53916600-53924000	Weak transcription	Psoas Muscle	Psoas
5	chr3:53916600-53924000	Weak transcription	A549	lung
6	chr3:53916600-53924400	Weak transcription	Fetal Kidney	kidney
7	chr3:53916600-53924800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:53916600-53924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:53916600-53924800	Weak transcription	Aorta	Aorta
10	chr3:53916800-53923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:53916800-53923200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:53916800-53923400	Weak transcription	Fetal Brain Male	brain
13	chr3:53916800-53924000	Weak transcription	Stomach Mucosa	stomach
14	chr3:53916800-53924400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:53916800-53924600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:53916800-53924600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:53917000-53922400	Strong transcription	Brain Germinal Matrix	brain
18	chr3:53917000-53922800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:53917000-53923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:53917200-53922400	Strong transcription	Liver	Liver
21	chr3:53917200-53922400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:53917200-53922400	Strong transcription	Osteobl	bone
23	chr3:53917200-53922600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:53917200-53922600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:53917200-53922600	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:53917200-53922800	Strong transcription	Primary B cells from cord blood	blood
27	chr3:53917200-53922800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:53917200-53923000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:53917200-53923400	Strong transcription	Fetal Intestine Large	intestine
30	chr3:53917400-53922600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:53917400-53923200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:53917600-53922400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:53917600-53922600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:53917600-53922800	Strong transcription	Left Ventricle	heart
35	chr3:53917800-53922600	Strong transcription	HUVEC	blood vessel
36	chr3:53917800-53922800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr3:53918000-53922400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr3:53918000-53924800	Weak transcription	Esophagus	oesophagus
39	chr3:53918200-53922400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:53918200-53922600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:53918400-53922400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr3:53918400-53922400	Strong transcription	Adipose Nuclei	Adipose
43	chr3:53918400-53922600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:53918600-53922400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:53918600-53922600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:53918600-53922600	Strong transcription	NHDF-Ad	bronchial
47	chr3:53918800-53922400	Strong transcription	Hela-S3	cervix
48	chr3:53919200-53923200	Weak transcription	Right Ventricle	heart
49	chr3:53919400-53922400	Strong transcription	NHEK	skin
50	chr3:53919600-53922400	Weak transcription	Small Intestine	intestine

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