Variant report

Variant	rs901746
Chromosome Location	chr11:47260319-47260320
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47234544..47240299-chr11:47253173..47262641,20	MCF-7	breast:
2	chr11:47256660..47260798-chr11:47290143..47292249,4	K562	blood:
3	chr11:47257344..47261784-chr11:47428504..47430961,3	K562	blood:
4	chr11:47256660..47261423-chr11:47290143..47292492,5	K562	blood:
5	chr11:47257788..47261523-chr11:47268362..47272495,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165915	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000255197	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs10501321	0.94[ASW][hapmap];0.98[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1052373	0.90[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1055510	0.85[EUR][1000 genomes]
rs10742799	0.85[EUR][1000 genomes]
rs10742801	0.83[EUR][1000 genomes]
rs10838681	0.84[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes]
rs10838684	0.87[EUR][1000 genomes]
rs10838690	0.84[EUR][1000 genomes]
rs10838691	0.83[EUR][1000 genomes]
rs10838692	0.90[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs10838693	0.83[EUR][1000 genomes]
rs11039156	0.84[EUR][1000 genomes]
rs11039166	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs11039167	0.82[EUR][1000 genomes]
rs12575456	0.84[EUR][1000 genomes]
rs1375688	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs1449627	0.90[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1685404	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs2013867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2269434	0.89[CEU][hapmap]
rs2279239	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2957873	0.81[CHD][hapmap]
rs326214	0.88[ASW][hapmap];0.90[CEU][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs326222	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35677603	0.82[ASN][1000 genomes]
rs35879051	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3758669	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3758672	0.86[EUR][1000 genomes]
rs3758673	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3781621	0.84[EUR][1000 genomes]
rs3781622	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs3816725	0.90[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs3847502	0.84[EUR][1000 genomes]
rs4752822	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4752824	0.84[EUR][1000 genomes]
rs4752825	0.83[EUR][1000 genomes]
rs4752973	0.82[CHB][hapmap]
rs4752980	0.84[EUR][1000 genomes]
rs59663860	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61896050	0.84[EUR][1000 genomes]
rs6485746	0.81[EUR][1000 genomes]
rs7109147	0.81[EUR][1000 genomes]
rs7109203	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7120118	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7120957	0.84[EUR][1000 genomes]
rs7124955	0.85[CEU][hapmap];0.98[GIH][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs7127907	0.84[EUR][1000 genomes]
rs7129661	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7395581	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7940809	0.84[EUR][1000 genomes]
rs830085	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer 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	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs901746	PACSIN3	cis	Esophagus Mucosa	GTEx
rs901746	MTCH2	cis	cerebellum	SCAN
rs901746	ACP2	cis	Thyroid	GTEx
rs901746	DGKZ	cis	cerebellum	SCAN
rs901746	ACP2	cis	lymphoblastoid	seeQTL
rs901746	UBA52	trans	parietal	SCAN
rs901746	DDB2	cis	multi-tissue	Pritchard
rs901746	NR1H3	cis	lymphoblastoid	seeQTL
rs901746	ACP2	cis	multi-tissue	Pritchard
rs901746	ATG13	cis	cerebellum	SCAN
rs901746	NR1H3	cis	multi-tissue	Pritchard
rs901746	DDB2	cis	lymphoblastoid	seeQTL
rs901746	DDB2	cis	Lymphoblastoid	GTEx
rs901746	MADD	cis	cerebellum	SCAN
rs901746	MADD	cis	parietal	SCAN
rs901746	NR1H3	cis	parietal	SCAN
rs901746	MYBPC3	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47238600-47261000	Weak transcription	Small Intestine	intestine
3	chr11:47240200-47266600	Weak transcription	Fetal Brain Male	brain
4	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:47243600-47269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr11:47246600-47267800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:47247400-47267600	Strong transcription	Thymus	Thymus
8	chr11:47248200-47265200	Strong transcription	GM12878-XiMat	blood
9	chr11:47248600-47260800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:47254000-47264600	Strong transcription	Dnd41	blood
11	chr11:47254600-47267800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr11:47254800-47261000	Weak transcription	Ovary	ovary
13	chr11:47255400-47262000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr11:47255400-47269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:47255600-47264600	Strong transcription	HepG2	liver
16	chr11:47255600-47268800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:47255800-47267600	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr11:47256000-47260600	Weak transcription	Fetal Kidney	kidney
19	chr11:47256000-47268000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:47256200-47260400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:47256200-47260800	Strong transcription	Fetal Intestine Small	intestine
22	chr11:47256200-47267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:47256400-47260600	Weak transcription	Brain Angular Gyrus	brain
24	chr11:47256400-47261000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:47256400-47267800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:47256600-47261000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr11:47256800-47260800	Weak transcription	Stomach Mucosa	stomach
28	chr11:47256800-47268800	Strong transcription	Fetal Thymus	thymus
29	chr11:47257000-47260400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:47257000-47260800	Weak transcription	NH-A	brain
31	chr11:47257000-47261400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:47257200-47260400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:47257200-47260400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:47257200-47260600	Weak transcription	Fetal Heart	heart
35	chr11:47257200-47260800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr11:47257400-47260400	Weak transcription	Placenta	Placenta
37	chr11:47257400-47260800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr11:47257400-47262000	Strong transcription	HMEC	breast
39	chr11:47257800-47267800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:47257800-47268000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr11:47258000-47262600	Strong transcription	HSMMtube	muscle
42	chr11:47258000-47269000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:47258200-47261000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:47258200-47263600	Strong transcription	NHLF	lung
45	chr11:47258200-47267600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:47258400-47263200	Strong transcription	Osteobl	bone
47	chr11:47258400-47266400	Strong transcription	Fetal Intestine Large	intestine
48	chr11:47258400-47267800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:47258400-47268400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:47258600-47261200	Weak transcription	Primary B cells from cord blood	blood

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