Variant report

Variant	rs630055
Chromosome Location	chr11:65087533-65087534
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65027863..65030554-chr11:65086504..65088006,2	K562	blood:
2	chr11:65085057..65089903-chr11:65095302..65099017,4	MCF-7	breast:
3	chr11:65044236..65045803-chr11:65087151..65090108,2	MCF-7	breast:
4	chr11:65082240..65084133-chr11:65085882..65087992,2	MCF-7	breast:
5	chr11:65085883..65088356-chr11:65092626..65095231,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149798	Chromatin interaction
ENSG00000014138	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1152611	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1195733	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs12269727	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1633466	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs1783486	0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs1858783	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239261	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs28781278	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2904966	1.00[CHB][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs2904967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2904979	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2904980	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap]
rs2904982	1.00[CHB][hapmap]
rs2904984	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs2904986	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3015997	0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs3016000	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741386	1.00[CHB][hapmap]
rs4149813	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs482842	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487568	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488289	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499027	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs503277	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507005	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509303	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs526502	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs542142	0.83[ASN][1000 genomes]
rs551523	1.00[CHB][hapmap]
rs554122	0.83[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap]
rs560097	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs592050	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603286	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs611910	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs612392	0.83[CHD][hapmap]
rs620427	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs626555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs626802	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636928	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs655433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667341	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668735	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs673147	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676114	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs676573	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs689288	0.83[CHD][hapmap]
rs7116674	0.94[CHD][hapmap]
rs8638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
4	nsv897714	chr11:65076918-65091609	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
6	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs630055	EFEMP2	cis	cerebellum	SCAN
rs630055	BANF1	cis	parietal	SCAN
rs630055	BATF2	cis	cerebellum	SCAN
rs630055	GAL3ST3	cis	cerebellum	SCAN
rs630055	SNORD27	cis	parietal	SCAN
rs630055	PLCB3	cis	cerebellum	SCAN
rs630055	POLA2	cis	multi-tissue	Pritchard
rs630055	RPS6KB2	cis	cerebellum	SCAN
rs630055	POLA2	cis	parietal	SCAN
rs630055	POLA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65083200-65093400	Weak transcription	Aorta	Aorta
2	chr11:65083400-65087800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:65083600-65096600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:65083800-65088400	Weak transcription	Small Intestine	intestine
5	chr11:65083800-65096600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:65084000-65088400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:65084400-65088600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:65084600-65088200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:65084800-65088000	Weak transcription	Brain Angular Gyrus	brain
10	chr11:65084800-65088200	Weak transcription	Esophagus	oesophagus
11	chr11:65085000-65088000	Weak transcription	Right Ventricle	heart
12	chr11:65085000-65088200	Weak transcription	Fetal Brain Female	brain
13	chr11:65085000-65088200	Weak transcription	Right Atrium	heart
14	chr11:65085000-65090400	Genic enhancers	Fetal Muscle Leg	muscle
15	chr11:65085000-65100800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:65085200-65087800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:65085200-65087800	Weak transcription	HSMM	muscle
18	chr11:65085200-65088000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:65085200-65088000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:65085200-65088000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:65085200-65088000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:65085200-65088000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:65085200-65088000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:65085200-65088000	Weak transcription	Fetal Lung	lung
25	chr11:65085200-65088000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:65085200-65088000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:65085200-65088000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:65085200-65088000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr11:65085200-65088200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:65085200-65088200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:65085200-65088200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr11:65085200-65088200	Weak transcription	Brain Germinal Matrix	brain
33	chr11:65085200-65088200	Weak transcription	Pancreas	Pancrea
34	chr11:65085200-65088200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr11:65085200-65088200	Weak transcription	A549	lung
36	chr11:65085200-65088400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:65085200-65088400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr11:65085200-65089400	Weak transcription	NH-A	brain
39	chr11:65085200-65089600	Weak transcription	Brain Anterior Caudate	brain
40	chr11:65085200-65089800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:65085200-65090000	Weak transcription	K562	blood
42	chr11:65085200-65091400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:65085200-65097200	Weak transcription	Stomach Mucosa	stomach
44	chr11:65085200-65101000	Weak transcription	Fetal Kidney	kidney
45	chr11:65085400-65088000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:65085400-65088000	Weak transcription	HMEC	breast
47	chr11:65085400-65088200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr11:65085400-65088200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:65085400-65088200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:65085400-65097000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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