Variant report

Variant	rs2282611
Chromosome Location	chr11:76154846-76154847
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:76154682-76154956	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:76154799-76156952	Raji	blood:	n/a	n/a
3	POLR2A	chr11:76154201-76156325	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr11:76154650-76154919	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr11:76154180-76156269	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr11:76154577-76154874	K562	blood:	n/a	n/a
7	FOS	chr11:76154665-76154997	MCF10A-Er-Src	breast:	n/a	n/a
8	SPI1	chr11:76154846-76155356	HL-60	blood:	n/a	n/a
9	RFX5	chr11:76154791-76156310	Hela-S3	cervix:	n/a	chr11:76155751-76155760
10	IRF1	chr11:76154300-76156230	K562	blood:	n/a	chr11:76155752-76155761 chr11:76154821-76154834 chr11:76154918-76154927
11	POLR2A	chr11:76154664-76157161	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr11:76154557-76157360	IMR90	lung:	n/a	chr11:76156167-76156176
13	POLR2A	chr11:76153936-76157201	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:76154393-76156302	K562	blood:	n/a	n/a
15	MYC	chr11:76154713-76155022	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr11:76154686-76157275	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr11:76154734-76155014	Hela-S3	cervix:	n/a	n/a
18	SIX5	chr11:76154582-76156442	A549	lung:	n/a	chr11:76155829-76155838 chr11:76156021-76156030 chr11:76156019-76156028
19	POLR2A	chr11:76154344-76157089	GM12878	blood:	n/a	n/a
20	CHD1	chr11:76154698-76156181	GM12878	blood:	n/a	n/a
21	TBP	chr11:76154348-76156222	Hela-S3	cervix:	n/a	n/a
22	HCFC1	chr11:76154093-76157371	Hela-S3	cervix:	n/a	n/a
23	ATF1	chr11:76154648-76154944	K562	blood:	n/a	n/a
24	HEY1	chr11:76154642-76155022	K562	blood:	n/a	n/a
25	TBP	chr11:76154841-76156189	GM12878	blood:	n/a	n/a
26	MYC	chr11:76154746-76154956	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr11:76154213-76157130	K562	blood:	n/a	n/a
28	POLR2A	chr11:76154125-76156325	GM12891	blood:	n/a	n/a
29	IRF1	chr11:76154324-76156230	K562	blood:	n/a	chr11:76155752-76155761 chr11:76154821-76154834 chr11:76154918-76154927
30	REST	chr11:76154779-76157403	H1-neurons	neurons:	n/a	chr11:76156341-76156351
31	POLR2A	chr11:76154364-76157125	PBDE	blood:	n/a	n/a
32	FOS	chr11:76154592-76154947	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr11:76154616-76157275	IMR90	lung:	n/a	n/a
34	POLR2A	chr11:76154378-76155015	K562	blood:	n/a	n/a
35	POLR2A	chr11:76154317-76157098	K562	blood:	n/a	n/a
36	POLR2A	chr11:76154466-76157119	K562	blood:	n/a	n/a
37	POLR2A	chr11:76154323-76157141	GM12878	blood:	n/a	n/a
38	JUND	chr11:76154629-76155113	K562	blood:	n/a	n/a
39	POLR2A	chr11:76154154-76157292	H1-hESC	embryonic stem cell:	n/a	n/a
40	FOS	chr11:76154637-76154914	MCF10A-Er-Src	breast:	n/a	n/a
41	RELA	chr11:76154770-76156189	GM18505	blood:	n/a	n/a
42	TRIM28	chr11:76154608-76156216	K562	blood:	n/a	n/a
43	TBL1XR1	chr11:76154358-76155221	K562	blood:	n/a	n/a
44	POLR2A	chr11:76154693-76155015	K562	blood:	n/a	n/a
45	SIN3A	chr11:76154747-76157249	H1-hESC	embryonic stem cell:	n/a	chr11:76156342-76156351 chr11:76156304-76156317 chr11:76157027-76157036
46	POLR2A	chr11:76154386-76157090	GM18505	blood:	n/a	n/a
47	POLR2A	chr11:76154005-76155249	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr11:76154470-76157033	GM19099	blood:	n/a	n/a
49	SIN3A	chr11:76154766-76157144	GM12878	blood:	n/a	chr11:76156342-76156351 chr11:76156304-76156317 chr11:76157027-76157036
50	POLR2A	chr11:76154531-76156200	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:76090234..76093573-chr11:76154824..76158196,8	MCF-7	breast:
2	chr11:76070486..76072111-chr11:76154139..76156807,2	MCF-7	breast:
3	chr11:76124499..76126640-chr11:76152855..76155406,3	MCF-7	breast:
4	chr11:76089758..76095735-chr11:76153234..76157826,15	MCF-7	breast:
5	chr11:76090615..76095251-chr11:76152894..76157527,10	K562	blood:
6	chr11:76096828..76101087-chr11:76152871..76156603,6	MCF-7	breast:
7	chr11:76154138..76157007-chr17:62501424..62503777,2	MCF-7	breast:
8	chr11:76154597..76156492-chr11:76776948..76779266,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKRIR-1	chr11:76152384-76155841	NONHSAT023169
2	lnc-PRKRIR-1	chr11:76153117-76155724	ENSG00000255135.2

Variant related genes	Relation type
C11orf30	TF binding region
ENSG00000137492	Chromatin interaction
ENSG00000179240	Chromatin interaction
ENSG00000272301	Chromatin interaction
ENSG00000149260	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000108654	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10160382	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs10793167	0.84[CEU][hapmap]
rs17245270	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17450692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17749618	0.91[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1939467	0.91[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1939468	0.91[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2508740	0.81[GIH][hapmap]
rs2508741	0.80[GIH][hapmap]
rs3753051	0.91[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55904328	0.90[ASN][1000 genomes]
rs55975198	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56159348	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56294280	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56393414	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56394729	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58015965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59168723	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61894507	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61894512	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61894542	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61894543	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61894546	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7107442	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7115331	0.80[EUR][1000 genomes]
rs7116583	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7123361	0.91[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7125552	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72930511	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7927515	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7928373	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7936656	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938856	0.81[CHD][hapmap];0.92[MEX][hapmap]
rs7941790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7942257	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7949258	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7951867	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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	nsv1050713	chr11:76147085-76267117	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2282611	ARHGEF17	cis	cerebellum	SCAN
rs2282611	SLCO2B1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76152000-76155200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:76153800-76157400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr11:76153800-76157400	Active TSS	Right Atrium	heart
4	chr11:76153800-76158800	Active TSS	GM12878-XiMat	blood
5	chr11:76154000-76155000	Flanking Active TSS	Dnd41	blood
6	chr11:76154000-76157400	Active TSS	Left Ventricle	heart
7	chr11:76154000-76157600	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr11:76154000-76157600	Active TSS	K562	blood
9	chr11:76154200-76155000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:76154200-76155000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:76154200-76155000	Flanking Active TSS	Fetal Brain Female	brain
12	chr11:76154200-76155000	Flanking Active TSS	Hela-S3	cervix
13	chr11:76154200-76155600	ZNF genes & repeats	Fetal Heart	heart
14	chr11:76154200-76157600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr11:76154200-76157600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr11:76154200-76157600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:76154200-76157800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr11:76154200-76158000	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr11:76154400-76155000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:76154400-76155000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr11:76154400-76155000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:76154400-76155000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr11:76154400-76155000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr11:76154400-76155000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr11:76154400-76155000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr11:76154400-76155000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:76154400-76155000	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr11:76154400-76155000	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr11:76154400-76155000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr11:76154400-76155000	Flanking Active TSS	Fetal Brain Male	brain
31	chr11:76154400-76155000	Flanking Active TSS	Fetal Kidney	kidney
32	chr11:76154400-76155000	Flanking Active TSS	Fetal Lung	lung
33	chr11:76154400-76155000	Flanking Active TSS	Fetal Stomach	stomach
34	chr11:76154400-76155000	Enhancers	Spleen	Spleen
35	chr11:76154400-76155000	Flanking Active TSS	HUVEC	blood vessel
36	chr11:76154400-76155200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:76154400-76155200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr11:76154400-76155200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:76154400-76155200	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr11:76154400-76155200	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr11:76154400-76155200	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr11:76154400-76155200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr11:76154400-76155200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr11:76154400-76155400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr11:76154400-76155400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr11:76154400-76155400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:76154400-76155400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:76154400-76155400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:76154400-76155400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr11:76154400-76156000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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