Variant report

Variant	rs9309267
Chromosome Location	chr2:55850333-55850334
allele	C/T
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	chr2:55850240-55850464	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55843280..55846696-chr2:55847912..55852861,6	MCF-7	breast:
2	chr2:55848892..55851384-chr2:55854717..55856988,2	MCF-7	breast:

Variant related genes	Relation type
SMEK2	TF binding region
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10172181	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10172506	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10173150	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10182131	0.88[AMR][1000 genomes]
rs10194634	0.83[AMR][1000 genomes]
rs10195281	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10200159	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203953	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204169	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10221888	0.82[YRI][hapmap]
rs10427222	0.86[YRI][hapmap]
rs1045920	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496044	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10496049	0.89[YRI][hapmap]
rs11676573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900763	0.86[YRI][hapmap]
rs11902712	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12615063	1.00[CHB][hapmap];0.88[AMR][1000 genomes]
rs12616502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616982	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12622830	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12623625	0.88[AMR][1000 genomes]
rs12989898	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs13028892	0.86[YRI][hapmap]
rs13382187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13383352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13399762	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13400946	0.88[AMR][1000 genomes]
rs13407344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13420929	0.88[AMR][1000 genomes]
rs13428382	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13428486	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430684	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17047094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17047119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867964	0.88[AMR][1000 genomes]
rs3748945	0.96[YRI][hapmap]
rs3748955	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816489	0.86[YRI][hapmap]
rs4671248	0.89[LWK][hapmap];0.86[YRI][hapmap]
rs6545507	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545508	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6545509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545512	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545513	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6705295	0.83[AMR][1000 genomes]
rs6712314	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717574	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6725101	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6736996	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739788	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6745430	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6745650	0.96[YRI][hapmap]
rs6760959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730884	0.87[AFR][1000 genomes]
rs736345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs744514	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7558127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7567115	0.88[AMR][1000 genomes]
rs7574398	0.85[AFR][1000 genomes]
rs7575906	0.88[AMR][1000 genomes]
rs7582174	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586115	0.88[AMR][1000 genomes]
rs7586124	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586366	0.88[AMR][1000 genomes]
rs7594212	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7594497	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9309268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9636439	0.85[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][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	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9309267	SLC22A6	trans	brain	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55850400	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr2:55846600-55851600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:55846600-55852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
10	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:55846800-55850400	Enhancers	Liver	Liver
13	chr2:55846800-55851200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:55846800-55853000	Weak transcription	A549	lung
15	chr2:55846800-55858200	Weak transcription	HSMM	muscle
16	chr2:55846800-55862000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:55846800-55862000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:55846800-55862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:55846800-55862600	Weak transcription	NHDF-Ad	bronchial
20	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
21	chr2:55846800-55863400	Weak transcription	NHLF	lung
22	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:55847000-55852600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr2:55847400-55852400	Weak transcription	HMEC	breast
26	chr2:55847400-55852800	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr2:55847400-55859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:55847400-55862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:55847600-55852400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:55847600-55852600	Weak transcription	Brain Anterior Caudate	brain
32	chr2:55847600-55852600	Weak transcription	Right Atrium	heart
33	chr2:55847600-55857400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:55847600-55860800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:55847600-55862000	Weak transcription	Osteobl	bone
36	chr2:55847600-55864200	Weak transcription	Brain Germinal Matrix	brain
37	chr2:55847600-55870000	Weak transcription	Colonic Mucosa	Colon
38	chr2:55847600-55870000	Weak transcription	Psoas Muscle	Psoas
39	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
40	chr2:55847800-55850400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:55847800-55850400	Genic enhancers	Dnd41	blood
42	chr2:55847800-55850600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr2:55847800-55852400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:55847800-55852400	Weak transcription	NHEK	skin
45	chr2:55847800-55852600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:55847800-55859000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:55847800-55862000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:55847800-55862000	Weak transcription	NH-A	brain
49	chr2:55847800-55862200	Weak transcription	HUVEC	blood vessel
50	chr2:55847800-55863400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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