Variant report

Variant	rs518162
Chromosome Location	chr11:101000501-101000502
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	EGR1	chr11:101000363-101000630	K562	blood:	n/a	n/a
2	SIN3A	chr11:100999815-101000698	H1-hESC	embryonic stem cell:	n/a	chr11:100999966-100999979
3	TAF1	chr11:101000323-101000603	K562	blood:	n/a	n/a
4	SIN3AK20	chr11:100999854-101000834	MCF-7	breast:	n/a	n/a
5	EGR1	chr11:101000258-101000689	MCF-7	breast:	n/a	chr11:101000286-101000301 chr11:101000287-101000300
6	POLR2A	chr11:100998760-101000535	ProgFib	skin:	n/a	n/a
7	MAX	chr11:100999554-101000708	MCF-7	breast:	n/a	n/a
8	EGR1	chr11:100999846-101000569	ECC-1	luminal epithelium:	n/a	chr11:100999949-100999962 chr11:100999948-100999958 chr11:101000286-101000301 chr11:101000287-101000300 chr11:100999943-100999956
9	POLR2A	chr11:100996140-101000814	MCF-7	breast:	n/a	n/a
10	FOXA1	chr11:101000348-101000695	T-47D	breast:	n/a	n/a
11	EGR1	chr11:101000320-101000735	K562	blood:	n/a	n/a
12	MAX	chr11:100999934-101000728	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr11:101000260-101000626	K562	blood:	n/a	n/a
14	SUZ12	chr11:100998043-101000691	NT2-D1	testis:	n/a	n/a
15	ZNF217	chr11:101000370-101000700	MCF-7	breast:	n/a	n/a
16	POLR2A	chr11:100998094-101000656	MCF-7	breast:	n/a	n/a
17	CTBP2	chr11:100999654-101000641	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF263	chr11:100998026-101000643	HEK293-T-REx	kidney:	n/a	chr11:100999852-100999861 chr11:101000568-101000577 chr11:100999855-100999864 chr11:100999821-100999830
19	TBP	chr11:101000344-101000644	K562	blood:	n/a	n/a
20	GATA3	chr11:101000037-101000501	MCF-7	breast:	n/a	n/a
21	MAZ	chr11:101000391-101000768	K562	blood:	n/a	n/a
22	GATA3	chr11:101000032-101000740	T-47D	breast:	n/a	n/a
23	MYC	chr11:100999638-101000628	K562	blood:	n/a	n/a
24	FOXA1	chr11:101000256-101000731	T-47D	breast:	n/a	n/a
25	TCF7L2	chr11:101000222-101000636	MCF-7	breast:	n/a	n/a
26	POLR2A	chr11:100998082-101000667	MCF-7	breast:	n/a	n/a
27	MAX	chr11:100999557-101000588	K562	blood:	n/a	n/a
28	HDAC2	chr11:101000280-101000714	MCF-7	breast:	n/a	n/a
29	POLR2A	chr11:101000074-101000601	K562	blood:	n/a	n/a
30	GATA3	chr11:100999799-101000710	T-47D	breast:	n/a	n/a
31	HA-E2F1	chr11:100997847-101000686	MCF-7	breast:	n/a	chr11:100999948-100999957 chr11:100999948-100999960 chr11:100998100-100998110
32	ESR1	chr11:101000309-101000617	T-47D	breast:	n/a	n/a
33	MAX	chr11:100999548-101000536	ECC-1	luminal epithelium:	n/a	n/a
34	MYC	chr11:101000420-101000554	MCF-7	breast:	n/a	n/a
35	SUZ12	chr11:100997669-101000621	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:100933625..100935266-chr11:100997720..101000555,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM133-3	chr11:100999808-101000619	NONHSAT023850
2	lnc-TMEM133-3	chr11:100999808-101000619	NONHSAT023851

Variant related genes	Relation type
PGR	TF binding region
ENSG00000082175	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11571271	0.82[MEX][hapmap]
rs1783747	1.00[JPT][hapmap]
rs477151	1.00[ASN][1000 genomes]
rs495997	1.00[JPT][hapmap]
rs503194	1.00[ASN][1000 genomes]
rs503362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs514469	0.83[AMR][1000 genomes]
rs518300	1.00[ASN][1000 genomes]
rs534200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs545845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs580512	1.00[ASN][1000 genomes]
rs582691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs601040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs658370	1.00[ASN][1000 genomes]
rs660149	1.00[JPT][hapmap]

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	nsv1048356	chr11:100713096-101058995	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv541154	chr11:100713096-101058995	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv556131	chr11:100985777-101480017	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898328	chr11:100993846-101009933	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100996600-101000600	Active TSS	Aorta	Aorta
2	chr11:100996600-101000600	Active TSS	K562	blood
3	chr11:100996600-101000800	Active TSS	Ovary	ovary
4	chr11:100996600-101001200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr11:100996800-101000800	Active TSS	Colon Smooth Muscle	Colon
6	chr11:100997200-101000600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr11:100997200-101000600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr11:100997400-101000600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr11:100997400-101000600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr11:100997400-101000600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr11:100997600-101000600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr11:100997600-101000600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr11:100997600-101000600	Active TSS	Left Ventricle	heart
14	chr11:100997600-101000600	Bivalent/Poised TSS	Psoas Muscle	Psoas
15	chr11:100997600-101000600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
16	chr11:100997600-101000800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:100997800-101000600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
18	chr11:100997800-101000600	Bivalent Enhancer	Fetal Brain Male	brain
19	chr11:100998800-101000600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr11:100998800-101000600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
21	chr11:100998800-101000600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
22	chr11:100998800-101000800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
23	chr11:100998800-101000800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
24	chr11:100999000-101000600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:100999200-101000600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:100999200-101000600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
27	chr11:100999200-101000600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
28	chr11:100999200-101000600	Bivalent/Poised TSS	NHLF	lung
29	chr11:100999400-101000600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
30	chr11:100999400-101000600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:100999400-101000600	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr11:100999400-101000600	Bivalent Enhancer	Fetal Stomach	stomach
33	chr11:100999400-101000600	Enhancers	Pancreas	Pancrea
34	chr11:100999400-101000600	Bivalent/Poised TSS	NHDF-Ad	bronchial
35	chr11:100999800-101000600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr11:100999800-101000600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr11:100999800-101000600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:100999800-101000600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr11:100999800-101000600	Bivalent Enhancer	Liver	Liver
40	chr11:100999800-101000800	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr11:100999800-101000800	Active TSS	Right Ventricle	heart
42	chr11:101000000-101000600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:101000000-101000600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
44	chr11:101000000-101000600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:101000000-101000600	Bivalent/Poised TSS	Fetal Brain Female	brain
46	chr11:101000000-101000800	Active TSS	Right Atrium	heart
47	chr11:101000200-101000600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr11:101000200-101000600	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr11:101000200-101000600	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:101000200-101000600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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