Variant report

Variant	rs1938590
Chromosome Location	chr11:58911452-58911453
allele	G/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	MXI1	chr11:58911027-58913404	IMR90	lung:	n/a	n/a
2	POLR2A	chr11:58911418-58912899	GM12878	blood:	n/a	n/a
3	TCF7L2	chr11:58911264-58911516	HepG2	liver:	n/a	n/a
4	CEBPB	chr11:58911230-58911467	HepG2	liver:	n/a	chr11:58911317-58911328
5	POLR2A	chr11:58909722-58913181	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:58911373-58912958	GM12878	blood:	n/a	n/a
7	GATA3	chr11:58911388-58911516	SH-SY5Y	brain:	n/a	n/a
8	TCF7L2	chr11:58911107-58911497	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr11:58911394-58912803	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:58909979-58911672	MCF10A-Er-Src	breast:	n/a	n/a
11	IRF1	chr11:58909985-58912557	K562	blood:	n/a	chr11:58910357-58910371 chr11:58912180-58912194 chr11:58910357-58910370 chr11:58911818-58911829 chr11:58911816-58911830 chr11:58910358-58910372 chr11:58910364-58910381 chr11:58910357-58910368 chr11:58910356-58910367 chr11:58910354-58910371 chr11:58910568-58910577 chr11:58910352-58910369 chr11:58912184-58912194 chr11:58912184-58912195 chr11:58910357-58910370 chr11:58912021-58912030 chr11:58910358-58910368 chr11:58912183-58912195 chr11:58910352-58910373 chr11:58910362-58910382 chr11:58912184-58912198 chr11:58910357-58910370 chr11:58912178-58912199 chr11:58910357-58910369 chr11:58910356-58910376 chr11:58910358-58910375
12	JUN	chr11:58911409-58911580	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58911158..58913877-chr11:58937423..58939058,2	K562	blood:
2	chr11:58904183..58908174-chr11:58910132..58913359,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245571	TF binding region
ENSG00000255381	TF binding region
FAM111A	TF binding region
ENSG00000245571	Chromatin interaction
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10792220	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896919	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229864	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs12280905	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2096543	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2845559	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4287350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4382926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4939257	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs540268	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs556507	0.86[ASN][1000 genomes]
rs587617	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs592110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610764	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs680661	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7939969	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1938590	LRRN4CL	cis	cerebellum	SCAN
rs1938590	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs1938590	OR5W2	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58908800-58913600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:58909400-58912000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:58909400-58912200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:58909400-58913200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr11:58909400-58913400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:58909400-58913400	Active TSS	NHDF-Ad	bronchial
7	chr11:58909400-58914000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr11:58909600-58912000	Active TSS	Brain Germinal Matrix	brain
9	chr11:58909600-58912200	Active TSS	Psoas Muscle	Psoas
10	chr11:58909600-58912200	Active TSS	Right Atrium	heart
11	chr11:58909600-58912200	Active TSS	Right Ventricle	heart
12	chr11:58909600-58912600	Active TSS	Aorta	Aorta
13	chr11:58909600-58912600	Active TSS	HSMMtube	muscle
14	chr11:58909800-58911600	Active TSS	Duodenum Mucosa	Duodenum
15	chr11:58909800-58912200	Active TSS	Left Ventricle	heart
16	chr11:58909800-58912400	Active TSS	Rectal Smooth Muscle	rectum
17	chr11:58909800-58912600	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr11:58910000-58911600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:58910000-58912400	Active TSS	Fetal Brain Female	brain
20	chr11:58910200-58912000	Active TSS	Fetal Brain Male	brain
21	chr11:58910600-58912000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr11:58910600-58912200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr11:58910600-58913000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr11:58910600-58913000	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr11:58910600-58913200	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr11:58910600-58913400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr11:58910600-58913400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:58910600-58913400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:58910600-58913400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:58910800-58911600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:58910800-58912000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:58910800-58912200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:58910800-58912200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr11:58910800-58912200	Flanking Active TSS	Hela-S3	cervix
35	chr11:58910800-58912800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr11:58910800-58913000	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr11:58910800-58913400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:58910800-58913600	Flanking Active TSS	HUVEC	blood vessel
39	chr11:58910800-58914200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr11:58911000-58911600	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr11:58911000-58911600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:58911000-58911600	Weak transcription	Esophagus	oesophagus
43	chr11:58911000-58911600	Active TSS	Fetal Muscle Leg	muscle
44	chr11:58911000-58911600	Weak transcription	Gastric	stomach
45	chr11:58911000-58911600	Weak transcription	Pancreas	Pancrea
46	chr11:58911000-58911600	Weak transcription	Small Intestine	intestine
47	chr11:58911000-58911600	Weak transcription	Spleen	Spleen
48	chr11:58911000-58911800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:58911000-58911800	Enhancers	Primary B cells from peripheral blood	blood
50	chr11:58911000-58911800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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