Variant report

Variant	rs11119930
Chromosome Location	chr1:212586042-212586043
allele	A/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	YY1	chr1:212585489-212586069	GM12892	blood:	n/a	chr1:212585861-212585871
2	SPI1	chr1:212585695-212586093	GM12878	blood:	n/a	chr1:212585893-212585902
3	SPI1	chr1:212585656-212586048	GM12891	blood:	n/a	chr1:212585893-212585902
4	MAX	chr1:212586002-212586180	GM12878	blood:	n/a	n/a
5	WRNIP1	chr1:212585582-212586213	GM12878	blood:	n/a	n/a
6	SPI1	chr1:212585499-212586100	GM12878	blood:	n/a	chr1:212585893-212585902 chr1:212585519-212585532
7	YY1	chr1:212585568-212586089	GM12878	blood:	n/a	chr1:212585861-212585871

No.	Distal block	Cell Line	Cell type
1	chr1:212550848..212553114-chr1:212586010..212588532,2	MCF-7	breast:
2	chr1:212457988..212460167-chr1:212585002..212587734,2	MCF-7	breast:
3	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:

Variant related genes	Relation type
TMEM206	TF binding region
ENSG00000066027	Chromatin interaction
ENSG00000117691	Chromatin interaction
ENSG00000065600	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10863961	0.89[CHB][hapmap]
rs10863963	1.00[CHB][hapmap]
rs11119889	0.87[CEU][hapmap]
rs11119896	0.87[CEU][hapmap]
rs11119919	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs11119920	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs11119924	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11119929	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576437	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11576769	0.84[ASN][1000 genomes]
rs11580285	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11584189	0.82[ASN][1000 genomes]
rs11587555	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11588867	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11589817	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11590242	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11590672	0.89[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12060029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062818	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073991	0.87[CEU][hapmap]
rs12090970	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12095810	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12096035	1.00[CHB][hapmap]
rs12411213	0.96[ASN][1000 genomes]
rs12726409	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12727947	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12728266	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12734895	1.00[CHB][hapmap]
rs12736502	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12743785	0.86[CHB][hapmap]
rs12745269	1.00[CHB][hapmap]
rs12756678	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1470390	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs1493600	1.00[CHB][hapmap]
rs17018933	0.87[CEU][hapmap]
rs17721302	1.00[CHB][hapmap]
rs2120770	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2297306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358454	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs2884465	0.92[ASN][1000 genomes]
rs2884466	0.92[ASN][1000 genomes]
rs34080686	0.84[ASN][1000 genomes]
rs351399	0.87[CEU][hapmap]
rs411278	0.87[CEU][hapmap]
rs4951595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104831	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661987	1.00[CHB][hapmap]
rs6667199	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs72754339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518399	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7523303	0.87[CEU][hapmap]
rs7531219	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
2	chr1:212571000-212586200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:212577200-212586200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:212577200-212586200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:212577800-212586600	Strong transcription	Fetal Muscle Trunk	muscle
6	chr1:212579800-212587000	Weak transcription	Right Atrium	heart
7	chr1:212580600-212587200	Weak transcription	HSMMtube	muscle
8	chr1:212580800-212586200	Strong transcription	Fetal Stomach	stomach
9	chr1:212580800-212586600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:212580800-212587000	Weak transcription	NHDF-Ad	bronchial
11	chr1:212583200-212586800	Weak transcription	HMEC	breast
12	chr1:212583200-212587000	Weak transcription	Fetal Heart	heart
13	chr1:212583200-212587000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:212583400-212586800	Weak transcription	HUVEC	blood vessel
15	chr1:212583600-212586800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:212583600-212587000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:212583600-212587000	Weak transcription	Hela-S3	cervix
18	chr1:212583800-212586600	Weak transcription	Colonic Mucosa	Colon
19	chr1:212583800-212586600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:212583800-212587000	Weak transcription	Right Ventricle	heart
21	chr1:212583800-212587000	Weak transcription	A549	lung
22	chr1:212583800-212587000	Weak transcription	NH-A	brain
23	chr1:212584000-212587000	Weak transcription	Fetal Kidney	kidney
24	chr1:212584000-212587200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:212584000-212587400	Weak transcription	Ovary	ovary
26	chr1:212584200-212586400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:212584200-212586600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:212584200-212586800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:212584200-212586800	Weak transcription	Adipose Nuclei	Adipose
30	chr1:212584200-212586800	Weak transcription	Esophagus	oesophagus
31	chr1:212584200-212586800	Weak transcription	Placenta	Placenta
32	chr1:212584200-212587000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:212584200-212587000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:212584200-212587000	Weak transcription	NHLF	lung
35	chr1:212584200-212587200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:212584200-212587200	Weak transcription	Fetal Lung	lung
37	chr1:212584200-212587200	Weak transcription	Osteobl	bone
38	chr1:212584400-212586200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:212584400-212586200	Weak transcription	Fetal Brain Male	brain
40	chr1:212584400-212586200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:212584400-212586400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:212584400-212586400	Weak transcription	Fetal Intestine Small	intestine
43	chr1:212584400-212587000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:212584400-212587000	Weak transcription	Liver	Liver
45	chr1:212584400-212587000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:212584400-212587200	Weak transcription	Fetal Intestine Large	intestine
47	chr1:212584400-212587200	Weak transcription	Gastric	stomach
48	chr1:212584600-212586400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:212584600-212587200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:212584800-212586200	Weak transcription	Brain Germinal Matrix	brain

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