Variant report

Variant	rs667341
Chromosome Location	chr11:65050182-65050183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65048019..65050734-chr11:65061171..65064659,3	K562	blood:
2	chr11:65049088..65050806-chr11:65053610..65055291,2	K562	blood:
3	chr11:65028603..65032064-chr11:65049175..65051003,3	MCF-7	breast:
4	chr11:65049333..65051598-chr11:65082376..65084933,2	K562	blood:

Variant related genes	Relation type
ENSG00000014138	Chromatin interaction
ENSG00000149798	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1152611	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1195733	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12269727	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1633466	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1783486	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs1858783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239261	0.80[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs2904966	1.00[CHB][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs2904967	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs2904979	0.80[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs2904980	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2904981	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2904982	1.00[CHB][hapmap]
rs2904984	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2904986	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3015997	0.80[CEU][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs3015999	0.80[ASN][1000 genomes]
rs3016000	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3016001	0.81[EUR][1000 genomes]
rs3741386	1.00[CHB][hapmap]
rs4149813	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs482842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487568	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487989	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs488289	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs499027	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs503277	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs506280	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs507005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs509303	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs526502	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs542142	0.81[ASN][1000 genomes]
rs551523	1.00[CHB][hapmap]
rs554122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs560097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571128	0.83[EUR][1000 genomes]
rs592050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs603286	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.98[ASN][1000 genomes]
rs620427	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap]
rs625427	0.82[EUR][1000 genomes]
rs626555	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs626802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs630055	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]
rs636928	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs655433	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs673147	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs676114	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs676573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7116674	0.89[CHD][hapmap]
rs8638	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv976461	chr11:65000821-65054446	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs667341	POLA2	cis	lymphoblastoid	seeQTL
rs667341	POLA2	cis	cerebellum	SCAN
rs667341	GAL3ST3	cis	cerebellum	SCAN
rs667341	BATF2	cis	cerebellum	SCAN
rs667341	RPS6KB2	cis	cerebellum	SCAN
rs667341	POLA2	cis	parietal	SCAN
rs667341	PLCB3	cis	cerebellum	SCAN
rs667341	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs667341	POLA2	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65030200-65058800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65030600-65056800	Weak transcription	Right Atrium	heart
3	chr11:65030600-65058000	Weak transcription	Fetal Brain Male	brain
4	chr11:65030600-65058800	Weak transcription	Psoas Muscle	Psoas
5	chr11:65031200-65064800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:65031800-65058000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:65042400-65068800	Strong transcription	Fetal Thymus	thymus
8	chr11:65042800-65059000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:65042800-65065000	Strong transcription	Primary T cells from cord blood	blood
10	chr11:65042800-65072800	Strong transcription	Dnd41	blood
11	chr11:65043000-65066200	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr11:65043000-65067600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:65043200-65066400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:65043200-65066600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:65043400-65056000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:65043400-65056000	Weak transcription	Fetal Heart	heart
17	chr11:65043400-65056800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:65043400-65058200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:65043400-65059000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:65043400-65067200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr11:65043400-65067200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:65043600-65065000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:65043800-65058000	Strong transcription	K562	blood
24	chr11:65044000-65065600	Strong transcription	Thymus	Thymus
25	chr11:65044400-65058800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:65044400-65066200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:65044800-65050600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr11:65045000-65050200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:65045000-65050400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr11:65045000-65066600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr11:65045200-65050400	Strong transcription	Primary B cells from cord blood	blood
32	chr11:65045200-65050400	Strong transcription	Primary hematopoietic stem cells	blood
33	chr11:65045200-65052000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr11:65045600-65065200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr11:65045800-65067200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:65046000-65067000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr11:65046200-65050200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:65046200-65050400	Strong transcription	Liver	Liver
39	chr11:65046200-65050400	Strong transcription	Brain Germinal Matrix	brain
40	chr11:65046200-65050400	Strong transcription	HepG2	liver
41	chr11:65046200-65050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr11:65046200-65056000	Strong transcription	Fetal Stomach	stomach
43	chr11:65046400-65050600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr11:65046400-65050800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:65046800-65057400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr11:65046800-65058000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:65047200-65050400	Strong transcription	Brain Anterior Caudate	brain
48	chr11:65047400-65050200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr11:65047600-65050600	Strong transcription	Fetal Lung	lung
50	chr11:65047600-65064800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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