Variant report

Variant	rs19039
Chromosome Location	chr11:86003045-86003046
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	RAD21	chr11:86002782-86003130	K562	blood:	n/a	chr11:86003015-86003034
2	RAD21	chr11:86002770-86003238	GM12878	blood:	n/a	chr11:86003015-86003034
3	CTCF	chr11:86002940-86003090	HEEpiC	esophagus:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
4	CTCF	chr11:86002913-86003176	GM12878	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
5	CTCF	chr11:86002920-86003070	GM12875	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
6	CTCF	chr11:86002924-86003161	MCF-7	breast:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
7	CTCF	chr11:86002946-86003137	GM13976	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
8	CTCF	chr11:86002960-86003110	AG10803	skin:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
9	CTCF	chr11:86002960-86003110	HCM	heart:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
10	CTCF	chr11:86003000-86003150	HVMF	connective:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
11	RAD21	chr11:86002729-86003223	H1-hESC	embryonic stem cell:	n/a	chr11:86003015-86003034
12	JUND	chr11:86002590-86003069	HepG2	liver:	n/a	n/a
13	CTCF	chr11:86002960-86003110	GM12875	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
14	RAD21	chr11:86002749-86003220	GM12878	blood:	n/a	chr11:86003015-86003034
15	CTCF	chr11:86002960-86003110	RPTEC	kidney:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
16	CTCF	chr11:86002909-86003144	A549	lung:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
17	CHD2	chr11:86002929-86003246	GM12878	blood:	n/a	n/a
18	CTCF	chr11:86002935-86003148	Kidney_OC	kidney:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
19	CTCF	chr11:86002929-86003169	Lung_OC	lung:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
20	CTCF	chr11:86002995-86003072	H1-hESC	embryonic stem cell:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
21	CTCF	chr11:86002798-86003181	H1-hESC	embryonic stem cell:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
22	CTCF	chr11:86002940-86003090	HRE	kidney:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
23	RAD21	chr11:86002878-86003122	K562	blood:	n/a	chr11:86003015-86003034
24	RAD21	chr11:86002811-86003256	Hela-S3	cervix:	n/a	chr11:86003015-86003034
25	MAZ	chr11:86002870-86003359	GM12878	blood:	n/a	n/a
26	CTCF	chr11:86002960-86003110	NB4	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
27	CTCF	chr11:86002940-86003090	HPF	lung:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
28	CTCF	chr11:86002940-86003090	HUVEC	blood vessel:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
29	CTCF	chr11:86002884-86003115	A549	lung:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
30	HCFC1	chr11:86003004-86003204	K562	blood:	n/a	n/a
31	CTCF	chr11:86002980-86003130	NHEK	skin:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
32	CTCF	chr11:86002940-86003133	NHEK	skin:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
33	FOS	chr11:86002940-86003314	MCF10A-Er-Src	breast:	n/a	chr11:86003063-86003073 chr11:86003063-86003073 chr11:86003138-86003149 chr11:86003137-86003145
34	CTCF	chr11:86002905-86003198	Spleen_OC	spleen:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
35	CTCF	chr11:86002922-86003153	GM10266	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
36	RAD21	chr11:86002795-86003198	HepG2	liver:	n/a	chr11:86003015-86003034
37	CTCF	chr11:86003000-86003150	GM12801	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
38	CTCF	chr11:86002960-86003110	AoAF	blood vessel:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
39	CTCF	chr11:86002980-86003130	Hela-S3	cervix:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
40	CTCF	chr11:86002980-86003130	GM12866	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
41	CTCF	chr11:86002728-86003292	A549	lung:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
42	CTCF	chr11:86002980-86003130	GM12868	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
43	CTCF	chr11:86002812-86003209	ECC-1	luminal epithelium:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
44	CTCF	chr11:86002980-86003130	HPAF	blood vessel:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
45	MAFK	chr11:86002509-86003231	K562	blood:	n/a	chr11:86002642-86002657
46	CTCF	chr11:86002960-86003110	GM12873	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
47	CTCF	chr11:86002949-86003114	GM20000	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
48	RAD21	chr11:86002635-86003280	SK-N-SH_RA	brain:	n/a	chr11:86003015-86003034
49	CTCF	chr11:86002980-86003130	AG09309	skin:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
50	CTCF	chr11:86002924-86003136	GM19238	blood:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032

No.	Distal block	Cell Line	Cell type
1	chr11:85652279..85653016-chr11:86002549..86003329,2	K562	blood:
2	chr11:85652247..85653318-chr11:86002213..86003416,4	MCF-7	breast:
3	chr11:85996870..85999859-chr11:86001615..86003194,2	K562	blood:
4	chr11:86001868..86005047-chr11:86005098..86008545,3	K562	blood:
5	chr11:85997706..86000207-chr11:86001867..86004535,3	MCF-7	breast:
6	chr11:85971469..85973576-chr11:86002289..86004505,2	MCF-7	breast:
7	chr11:85565171..85567495-chr11:86001547..86003230,2	K562	blood:
8	chr11:85990195..85992374-chr11:86002425..86005252,2	K562	blood:
9	chr11:85565405..85566629-chr11:86002540..86003473,8	K562	blood:
10	chr11:85989760..85992310-chr11:86001977..86004661,2	MCF-7	breast:

Variant related genes	Relation type
SETP17	TF binding region
ENSG00000150676	Chromatin interaction
ENSG00000215504	Chromatin interaction
ENSG00000255222	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10751138	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10792840	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792847	0.81[TSI][hapmap]
rs10898450	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898454	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898455	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898456	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11234582	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs11234583	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11234585	0.86[ASN][1000 genomes]
rs11234586	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11234587	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11234591	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11234592	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11234595	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11234621	0.80[ASN][1000 genomes]
rs11825046	0.80[ASN][1000 genomes]
rs1215001	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225782	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12226796	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12282663	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12574118	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12577739	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12800606	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1376947	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1391221	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2173281	0.82[CHD][hapmap]
rs2600950	0.81[AMR][1000 genomes]
rs2600951	0.81[TSI][hapmap]
rs2646727	0.81[TSI][hapmap]
rs2646732	0.82[ASN][1000 genomes]
rs2847470	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2847471	0.81[TSI][hapmap]
rs291203	0.82[ASN][1000 genomes]
rs291215	0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs291216	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs291220	0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs291221	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs291225	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs291227	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291228	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291230	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291231	0.96[CEU][hapmap];0.81[CHD][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs291232	0.95[EUR][1000 genomes]
rs291233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291235	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs291236	0.88[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs291237	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs291238	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs291242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs291247	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs291251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs291252	0.80[TSI][hapmap]
rs34095340	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34972740	0.86[ASN][1000 genomes]
rs3923738	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4547120	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944562	0.90[EUR][1000 genomes]
rs7106569	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs7480354	0.80[ASN][1000 genomes]
rs7937597	0.80[ASN][1000 genomes]
rs7948056	0.80[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	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv508643	chr11:85988577-86047719	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs19039	EED	cis	parietal	SCAN
rs19039	EED	Cis_1M	lymphoblastoid	RTeQTL
rs19039	LRRC58	trans	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85957400-86008000	Weak transcription	Psoas Muscle	Psoas
2	chr11:85991400-86003200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:85992200-86003200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:85995600-86012600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:85995600-86012800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:85995800-86012600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:85995800-86013200	Weak transcription	Esophagus	oesophagus
8	chr11:85995800-86013200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:85996000-86012800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:85996000-86013000	Weak transcription	Fetal Intestine Large	intestine
11	chr11:86000200-86003800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:86000400-86005400	Enhancers	GM12878-XiMat	blood
13	chr11:86001000-86003200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:86001000-86004400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:86001000-86004800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:86001200-86005200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:86001800-86003400	Enhancers	Liver	Liver
18	chr11:86002400-86003200	Enhancers	HepG2	liver
19	chr11:86002400-86005400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:86002600-86003400	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr11:86002600-86003400	Enhancers	Hela-S3	cervix
22	chr11:86002600-86003400	Enhancers	HMEC	breast
23	chr11:86002600-86003400	Enhancers	Osteobl	bone
24	chr11:86002600-86004600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr11:86002600-86005400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:86002800-86003200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr11:86002800-86003200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:86002800-86004600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:86002800-86004600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr11:86003000-86003200	Enhancers	NH-A	brain
31	chr11:86003000-86003200	Enhancers	NHLF	lung
32	chr11:86003000-86003400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr11:86003000-86004200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr11:86003000-86012600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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