Variant report

Variant	rs947941
Chromosome Location	chr11:66822779-66822780
allele	A/G
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	ZKSCAN1	chr11:66821373-66823105	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr11:66821945-66822859	HepG2	liver:	n/a	chr11:66822577-66822586
3	FOXA1	chr11:66822391-66822858	T-47D	breast:	n/a	n/a
4	ZNF217	chr11:66822340-66823510	MCF-7	breast:	n/a	n/a
5	FOS	chr11:66822024-66822909	MCF10A-Er-Src	breast:	n/a	chr11:66822186-66822196
6	NFYA	chr11:66822035-66822835	Hela-S3	cervix:	n/a	n/a
7	MAZ	chr11:66822212-66822972	HepG2	liver:	n/a	chr11:66822579-66822587
8	MAX	chr11:66822102-66822964	K562	blood:	n/a	chr11:66822579-66822587
9	POLR2A	chr11:66821984-66825368	MCF10A-Er-Src	breast:	n/a	n/a
10	RFX5	chr11:66821964-66825080	Hela-S3	cervix:	n/a	n/a
11	USF1	chr11:66822386-66822900	A549	lung:	n/a	n/a
12	TBP	chr11:66822001-66823517	Hela-S3	cervix:	n/a	n/a
13	FOS	chr11:66822013-66822874	MCF10A-Er-Src	breast:	n/a	chr11:66822186-66822196
14	MAZ	chr11:66821325-66825015	Hela-S3	cervix:	n/a	chr11:66821651-66821662 chr11:66822579-66822587 chr11:66824076-66824086
15	MYC	chr11:66822015-66823668	MCF10A-Er-Src	breast:	n/a	chr11:66822579-66822587
16	TFAP2A	chr11:66822388-66823104	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr11:66822123-66822851	SK-N-SH	brain:	n/a	chr11:66822577-66822586
18	EGR1	chr11:66822387-66823894	MCF-7	breast:	n/a	chr11:66823429-66823444 chr11:66823430-66823443 chr11:66823430-66823443 chr11:66823430-66823443 chr11:66823432-66823442 chr11:66823431-66823442 chr11:66823430-66823444 chr11:66823433-66823443 chr11:66823433-66823442 chr11:66823430-66823443 chr11:66823432-66823442 chr11:66823431-66823445
19	STAT3	chr11:66822102-66822852	Hela-S3	cervix:	n/a	n/a
20	E2F4	chr11:66822534-66822836	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr11:66821969-66824640	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr11:66822704-66824521	MCF10A-Er-Src	breast:	n/a	n/a
23	MAX	chr11:66822100-66823918	MCF-7	breast:	n/a	chr11:66822579-66822587
24	CREB1	chr11:66821951-66822993	A549	lung:	n/a	n/a
25	MAX	chr11:66821980-66822966	A549	lung:	n/a	chr11:66822579-66822587
26	SP1	chr11:66822370-66822903	HepG2	liver:	n/a	chr11:66822849-66822858 chr11:66822822-66822831 chr11:66822817-66822831 chr11:66822821-66822831 chr11:66822820-66822832 chr11:66822821-66822830 chr11:66822820-66822832 chr11:66822848-66822857 chr11:66822849-66822858 chr11:66822821-66822831
27	GATA3	chr11:66822439-66822817	MCF-7	breast:	n/a	n/a
28	FOXA2	chr11:66822402-66822805	HepG2	liver:	n/a	n/a
29	SMARCC1	chr11:66821289-66824184	Hela-S3	cervix:	n/a	n/a
30	GATA3	chr11:66822163-66823730	MCF-7	breast:	n/a	n/a
31	FOXA2	chr11:66822352-66822984	A549	lung:	n/a	n/a
32	NR3C1	chr11:66821934-66822927	A549	lung:	n/a	n/a
33	GTF2F1	chr11:66822060-66823863	Hela-S3	cervix:	n/a	n/a
34	TFAP2C	chr11:66821330-66823836	Hela-S3	cervix:	n/a	n/a
35	TCF12	chr11:66822646-66824745	ECC-1	luminal epithelium:	n/a	chr11:66822932-66822942
36	GATA2	chr11:66822401-66822817	SH-SY5Y	brain:	n/a	n/a
37	MAX	chr11:66822477-66822890	K562	blood:	n/a	chr11:66822579-66822587
38	TCF7L2	chr11:66821375-66823720	Hela-S3	cervix:	n/a	n/a
39	SIN3AK20	chr11:66822012-66824574	MCF-7	breast:	n/a	n/a
40	POLR2A	chr11:66821756-66823093	Hela-S3	cervix:	n/a	n/a
41	EP300	chr11:66822376-66822831	HepG2	liver:	n/a	chr11:66822659-66822666
42	FOXA1	chr11:66822433-66822890	HepG2	liver:	n/a	n/a
43	REST	chr11:66822344-66822944	A549	lung:	n/a	n/a
44	STAT1	chr11:66821381-66823065	Hela-S3	cervix:	n/a	chr11:66822099-66822108 chr11:66821434-66821442 chr11:66822100-66822109 chr11:66822097-66822111 chr11:66822085-66822108
45	CEBPB	chr11:66822226-66822911	A549	lung:	n/a	n/a
46	MAX	chr11:66821221-66823085	A549	lung:	n/a	chr11:66821651-66821662 chr11:66822579-66822587
47	EP300	chr11:66821846-66823066	A549	lung:	n/a	chr11:66823008-66823024 chr11:66822023-66822033 chr11:66822038-66822048 chr11:66822659-66822666
48	FOS	chr11:66822019-66822815	MCF10A-Er-Src	breast:	n/a	chr11:66822186-66822196
49	NR3C1	chr11:66822450-66822933	A549	lung:	n/a	n/a
50	SMC3	chr11:66821284-66823873	Hela-S3	cervix:	n/a	chr11:66821493-66821507 chr11:66822741-66822751

No.	Distal block	Cell Line	Cell type
1	chr11:66820321..66823025-chr11:67079850..67082744,2	MCF-7	breast:
2	chr11:66764015..66766435-chr11:66822154..66824249,3	MCF-7	breast:
3	chr11:66820676..66825699-chr11:67004753..67010986,10	MCF-7	breast:
4	chr11:66620791..66624898-chr11:66820050..66822963,3	MCF-7	breast:
5	chr11:66821645..66823660-chr11:67007485..67010050,2	K562	blood:
6	chr11:66772471..66774496-chr11:66821395..66823474,2	MCF-7	breast:
7	chr11:66786143..66803039-chr11:66815769..66832347,160	MCF-7	breast:
8	chr11:66786222..66802522-chr11:66819452..66831805,83	MCF-7	breast:
9	chr11:66822423..66825123-chr11:67007249..67009585,3	MCF-7	breast:
10	chr11:66821776..66823454-chr11:66841539..66844484,2	K562	blood:
11	chr11:66821404..66826403-chr11:66884710..66889541,16	MCF-7	breast:
12	chr11:66821897..66826528-chr11:67139094..67144065,11	MCF-7	breast:
13	chr11:66821653..66823767-chr17:57968041..57970809,2	MCF-7	breast:
14	chr11:66610287..66613457-chr11:66821215..66824724,5	MCF-7	breast:
15	chr11:66761490..66778711-chr11:66821814..66832221,36	MCF-7	breast:
16	chr11:66821906..66824181-chr11:67166947..67168944,2	MCF-7	breast:
17	chr11:66820570..66825355-chr11:67030338..67035766,7	MCF-7	breast:
18	chr11:66822302..66823952-chr11:67266866..67269805,2	K562	blood:
19	chr11:66821940..66824182-chr11:67145187..67147338,3	MCF-7	breast:
20	chr11:66625545..66627133-chr11:66822302..66823974,2	MCF-7	breast:
21	chr11:66795170..66795767-chr11:66822449..66823273,3	MCF-7	breast:
22	chr11:66821441..66825228-chr11:67054009..67057657,5	MCF-7	breast:
23	chr11:66815902..66818882-chr11:66820733..66823960,3	K562	blood:
24	chr11:66822099..66824067-chr11:67083569..67086506,3	MCF-7	breast:
25	chr11:66821262..66823223-chr11:67083619..67086226,3	K562	blood:
26	chr11:66821625..66825972-chr11:66885437..66888104,7	MCF-7	breast:
27	chr11:66794994..66795751-chr11:66822067..66823335,6	MCF-7	breast:

Variant related genes	Relation type
RHOD	TF binding region
ENSG00000172932	Chromatin interaction
ENSG00000173653	Chromatin interaction
ENSG00000172531	Chromatin interaction
ENSG00000108443	Chromatin interaction
ENSG00000108423	Chromatin interaction
ENSG00000173020	Chromatin interaction
ENSG00000252709	Chromatin interaction
ENSG00000256514	Chromatin interaction
ENSG00000173120	Chromatin interaction
ENSG00000173621	Chromatin interaction
ENSG00000173227	Chromatin interaction
ENSG00000175505	Chromatin interaction
ENSG00000110697	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2260587	0.86[MKK][hapmap];1.00[TSI][hapmap]
rs2513660	1.00[AMR][1000 genomes]
rs45620032	1.00[AMR][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	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
3	esv1817552	chr11:66751014-66839985	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv532287	chr11:66784014-67023899	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs947941	HDGFRP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66813600-66823400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:66816800-66823400	Weak transcription	NHDF-Ad	bronchial
3	chr11:66819600-66823200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:66820200-66823600	Enhancers	Pancreas	Pancrea
5	chr11:66820200-66823800	Enhancers	Stomach Mucosa	stomach
6	chr11:66820400-66822800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:66820400-66823600	Enhancers	Esophagus	oesophagus
8	chr11:66820600-66822800	Enhancers	NHEK	skin
9	chr11:66820600-66823000	Enhancers	Placenta	Placenta
10	chr11:66820600-66823200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:66820800-66822800	Enhancers	Duodenum Mucosa	Duodenum
12	chr11:66820800-66822800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr11:66820800-66823000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr11:66820800-66823600	Enhancers	Liver	Liver
15	chr11:66821200-66822800	Enhancers	HMEC	breast
16	chr11:66821200-66823000	Enhancers	Fetal Intestine Small	intestine
17	chr11:66821200-66823800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:66821200-66823800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:66821200-66823800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:66821400-66823000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:66821400-66823000	Enhancers	NH-A	brain
22	chr11:66821400-66823200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:66821400-66823200	Enhancers	Ovary	ovary
24	chr11:66821400-66823200	Enhancers	NHLF	lung
25	chr11:66821400-66823400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr11:66821400-66823400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
27	chr11:66821400-66823600	Enhancers	Fetal Heart	heart
28	chr11:66821400-66823600	Enhancers	HUVEC	blood vessel
29	chr11:66821400-66823800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:66821400-66823800	Bivalent Enhancer	Fetal Muscle Leg	muscle
31	chr11:66821400-66823800	Enhancers	Gastric	stomach
32	chr11:66821400-66823800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr11:66821600-66822800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:66821600-66822800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:66821600-66823000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr11:66821600-66823000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr11:66821600-66823600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:66821600-66823600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:66821600-66823600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr11:66821600-66823600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr11:66821600-66823600	Enhancers	Brain Anterior Caudate	brain
42	chr11:66821600-66823600	Flanking Active TSS	HepG2	liver
43	chr11:66821600-66823800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:66821600-66823800	Enhancers	K562	blood
45	chr11:66821600-66824000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:66821600-66824800	Enhancers	HSMMtube	muscle
47	chr11:66821800-66822800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr11:66821800-66822800	Enhancers	Fetal Intestine Large	intestine
49	chr11:66821800-66822800	Enhancers	HSMM	muscle
50	chr11:66821800-66823000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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