Variant report

Variant	rs625938
Chromosome Location	chr11:75203699-75203700
allele	A/C
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	chr11:75203199-75203708	Raji	blood:	n/a	n/a
2	POLR2A	chr11:75203009-75203811	GM12892	blood:	n/a	n/a
3	RELA	chr11:75203233-75203704	GM12891	blood:	n/a	n/a
4	POLR2A	chr11:75203167-75203724	HCT-116	colon:	n/a	n/a
5	POLR2A	chr11:75202996-75203819	GM12892	blood:	n/a	n/a
6	SPI1	chr11:75203180-75203753	HL-60	blood:	n/a	chr11:75203451-75203460 chr11:75203449-75203462 chr11:75203305-75203318
7	SMARCC1	chr11:75202992-75203774	Hela-S3	cervix:	n/a	chr11:75203420-75203429
8	GABPA	chr11:75203166-75203746	HL-60	blood:	n/a	n/a
9	GABPA	chr11:75203193-75203777	HL-60	blood:	n/a	n/a
10	SPI1	chr11:75203042-75203819	GM12878	blood:	n/a	chr11:75203451-75203460 chr11:75203449-75203462 chr11:75203305-75203318
11	RCOR1	chr11:75203485-75203720	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:75203244-75203712	GM12892	blood:	n/a	n/a
13	ELF1	chr11:75203171-75203705	MCF-7	breast:	n/a	chr11:75203195-75203207 chr11:75203450-75203461 chr11:75203448-75203461
14	POLR2A	chr11:75203210-75203756	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:75203200..75205117-chr11:75206279..75208422,2	MCF-7	breast:
2	chr11:75186423..75188493-chr11:75202325..75205145,2	K562	blood:
3	chr11:75202940..75204464-chr11:75209500..75211854,2	MCF-7	breast:

Variant related genes	Relation type
GDPD5	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1004856	0.85[AFR][1000 genomes]
rs10751243	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236441	0.81[AFR][1000 genomes]
rs1557474	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1623440	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1631865	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790145	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790149	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790153	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790154	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790155	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1790156	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790158	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790160	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1793411	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1793412	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1793414	0.86[AFR][1000 genomes]
rs1793415	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1894213	0.84[EUR][1000 genomes]
rs471857	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs473462	0.85[EUR][1000 genomes]
rs474056	0.84[EUR][1000 genomes]
rs482458	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs482503	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs486326	0.84[EUR][1000 genomes]
rs488305	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs492309	0.83[EUR][1000 genomes]
rs504685	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs518611	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs523617	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs532454	0.83[EUR][1000 genomes]
rs535520	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs535523	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs546632	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs547844	0.85[EUR][1000 genomes]
rs550957	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609793	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs611449	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs623338	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs628972	0.87[AFR][1000 genomes]
rs653673	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs668727	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897923	chr11:75129007-75302855	Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75190400-75207400	Weak transcription	Fetal Stomach	stomach
2	chr11:75199400-75207000	Weak transcription	Adipose Nuclei	Adipose
3	chr11:75199400-75209800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:75200000-75219600	Weak transcription	Fetal Brain Female	brain
5	chr11:75201000-75203800	Enhancers	HMEC	breast
6	chr11:75201000-75203800	Enhancers	HUVEC	blood vessel
7	chr11:75201200-75203800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr11:75201200-75203800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:75201400-75203800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr11:75201400-75203800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:75201400-75203800	Enhancers	NHEK	skin
12	chr11:75201400-75207000	Weak transcription	Fetal Intestine Large	intestine
13	chr11:75201600-75203800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:75201600-75204000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:75201800-75204400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:75201800-75206800	Weak transcription	HepG2	liver
17	chr11:75202000-75203800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:75202000-75207000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:75202000-75207000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:75202200-75203800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr11:75202200-75203800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr11:75202200-75207000	Weak transcription	HSMMtube	muscle
23	chr11:75202200-75207200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:75202200-75208800	Weak transcription	HSMM	muscle
25	chr11:75202400-75203800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr11:75202400-75203800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr11:75202400-75210000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:75202600-75204200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:75202600-75206800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:75202600-75207000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:75202800-75203800	Enhancers	Primary B cells from peripheral blood	blood
32	chr11:75202800-75203800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:75202800-75203800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:75202800-75203800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr11:75202800-75203800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:75202800-75204000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr11:75203000-75203800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr11:75203000-75203800	Enhancers	Primary T cells from cord blood	blood
39	chr11:75203000-75203800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:75203000-75203800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:75203000-75203800	Enhancers	Fetal Thymus	thymus
42	chr11:75203000-75203800	Flanking Active TSS	Hela-S3	cervix
43	chr11:75203000-75203800	Enhancers	K562	blood
44	chr11:75203000-75204000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr11:75203000-75204000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr11:75203000-75204200	Enhancers	Primary hematopoietic stem cells	blood
47	chr11:75203000-75204400	Enhancers	Spleen	Spleen
48	chr11:75203200-75203800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:75203200-75203800	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr11:75203200-75203800	Enhancers	Esophagus	oesophagus

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