Variant report

Variant	rs1631684
Chromosome Location	chr11:57420885-57420886
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	POLR2A	chr11:57410796-57421100	H1-hESC	embryonic stem cell:	n/a	n/a
2	SPI1	chr11:57420765-57420934	K562	blood:	n/a	n/a
3	POLR2A	chr11:57420204-57420990	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr11:57410821-57420904	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr11:57420823-57421055	NB4	blood:	n/a	chr11:57420894-57420904
6	ATF2	chr11:57420021-57420963	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr11:57420799-57421046	NB4	blood:	n/a	chr11:57420894-57420904
8	POLR2A	chr11:57420745-57421004	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr11:57420818-57420996	H1-hESC	embryonic stem cell:	n/a	n/a
10	REST	chr11:57420396-57420982	HL-60	blood:	n/a	chr11:57420478-57420487
11	MYC	chr11:57420848-57421022	K562	blood:	n/a	chr11:57420894-57420904
12	SPI1	chr11:57420616-57421092	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57415751..57417478-chr11:57419075..57422993,4	K562	blood:
2	chr11:57419081..57422303-chr11:57422733..57426519,4	K562	blood:
3	chr11:57420796..57422353-chr11:57423420..57425537,2	K562	blood:

Variant related genes	Relation type
YPEL4	TF binding region
CLP1	TF binding region
ENSG00000166793	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000254602	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10792110	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10896644	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10896649	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11229109	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs11570176	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11570181	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12270209	0.81[ASN][1000 genomes]
rs12274865	0.81[ASN][1000 genomes]
rs12363024	0.82[ASN][1000 genomes]
rs1424753	0.82[ASN][1000 genomes]
rs1613592	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1624389	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1647394	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1647403	0.88[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17455422	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17455626	0.82[ASN][1000 genomes]
rs1783818	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs1783826	1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs1783827	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783828	0.81[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783829	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1783976	0.82[ASN][1000 genomes]
rs1783978	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1783979	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1783980	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1783981	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1783983	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1783984	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1783985	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1785498	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1798172	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1798173	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1798177	0.81[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2156638	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2956981	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3017889	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs36036499	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4611222	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs627145	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs653889	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs665058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7105506	0.82[ASN][1000 genomes]
rs7115528	0.82[ASN][1000 genomes]
rs7117020	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7120868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7479922	0.82[ASN][1000 genomes]
rs7947357	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs929934	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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 target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1631684	YPEL4	cis	lung	GTEx
rs1631684	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57417800-57424600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:57417800-57424600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:57418000-57424200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:57418000-57424200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:57418000-57424200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:57418000-57424200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:57418000-57424400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:57418000-57424600	Weak transcription	Right Atrium	heart
9	chr11:57418000-57424600	Weak transcription	HSMM	muscle
10	chr11:57418200-57424200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:57418200-57424200	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:57418200-57424400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr11:57418400-57424600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:57418600-57424200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:57418600-57424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:57418800-57424600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:57419600-57422600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr11:57419800-57421600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr11:57420000-57421200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:57420200-57421000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr11:57420200-57421400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:57420200-57421600	Weak transcription	Placenta	Placenta
23	chr11:57420200-57424200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr11:57420400-57421000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr11:57420400-57421400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr11:57420400-57421400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr11:57420400-57421400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr11:57420400-57421400	Enhancers	Fetal Lung	lung
29	chr11:57420400-57424400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr11:57420400-57424400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:57420400-57424400	Weak transcription	Thymus	Thymus
32	chr11:57420600-57421000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:57420600-57421000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr11:57420600-57421400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:57420600-57421400	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr11:57420600-57421400	Enhancers	Primary B cells from cord blood	blood
37	chr11:57420600-57421600	Enhancers	Primary hematopoietic stem cells	blood
38	chr11:57420600-57424000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:57420600-57424000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr11:57420600-57424000	Weak transcription	Dnd41	blood
41	chr11:57420600-57424200	Weak transcription	Primary T cells from cord blood	blood
42	chr11:57420600-57424200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:57420600-57424200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr11:57420600-57424400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:57420600-57424400	Weak transcription	NHLF	lung
46	chr11:57420800-57421200	Weak transcription	Fetal Thymus	thymus
47	chr11:57420800-57421400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr11:57420800-57421400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:57420800-57421400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:57420800-57424000	Weak transcription	Duodenum Mucosa	Duodenum

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