Variant report

Variant	rs250232
Chromosome Location	chr5:50262508-50262509
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	POLR2A	chr5:50261628-50264919	H1-neurons	neurons:	n/a	n/a
2	SUZ12	chr5:50262485-50266469	NT2-D1	testis:	n/a	n/a
3	MAX	chr5:50262102-50262702	H1-hESC	embryonic stem cell:	n/a	chr5:50262423-50262439
4	TCF12	chr5:50262482-50262785	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr5:50262363-50262814	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr5:50261908-50262733	H1-hESC	embryonic stem cell:	n/a	n/a
7	SUZ12	chr5:50261520-50262806	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chr5:50261485-50263029	H1-hESC	embryonic stem cell:	n/a	n/a
9	SP1	chr5:50262054-50262893	H1-hESC	embryonic stem cell:	n/a	chr5:50262621-50262630 chr5:50262620-50262632 chr5:50262620-50262632 chr5:50262622-50262631
10	YY1	chr5:50261828-50262674	H1-hESC	embryonic stem cell:	n/a	chr5:50262619-50262630
11	MAX	chr5:50262029-50262607	H1-hESC	embryonic stem cell:	n/a	chr5:50262423-50262439
12	ZNF143	chr5:50262051-50262826	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr5:50261875-50264646	H1-neurons	neurons:	n/a	n/a
14	CTBP2	chr5:50261236-50262966	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr5:50261713-50266474	H1-neurons	neurons:	n/a	chr5:50264435-50264449 chr5:50264118-50264138 chr5:50264118-50264138 chr5:50265442-50265452 chr5:50264121-50264134
16	MAX	chr5:50262076-50262695	H1-hESC	embryonic stem cell:	n/a	chr5:50262423-50262439
17	JUND	chr5:50262060-50262810	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:38003355..38005334-chr5:50260049..50263278,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248918	TF binding region
ENSG00000100083	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1354171	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs1374037	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs173648	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs185136	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs192223	0.93[AFR][1000 genomes]
rs1993954	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250225	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250226	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250227	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250228	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250231	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250235	0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250239	0.87[AFR][1000 genomes]
rs250240	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250241	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250242	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250243	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs27276	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs31714	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs583124	0.84[AFR][1000 genomes]
rs583125	0.91[AFR][1000 genomes]
rs589372	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs602484	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs614328	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs630982	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs679678	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830286	chr5:50165805-50374600	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50258600-50266600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr5:50260200-50265000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:50261200-50262600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:50261400-50262800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:50261400-50263400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr5:50261400-50263600	Bivalent Enhancer	Fetal Intestine Large	intestine
7	chr5:50261400-50266400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:50261400-50266400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr5:50261600-50262800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:50261600-50262800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
11	chr5:50261600-50263000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:50261600-50263200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:50261600-50263200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
14	chr5:50261600-50263200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
15	chr5:50261600-50263200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:50261600-50263200	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr5:50261600-50263400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr5:50261600-50263400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr5:50261600-50263400	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr5:50261600-50264400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr5:50261800-50262800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
22	chr5:50261800-50263000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:50261800-50263200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:50261800-50263400	Bivalent Enhancer	Liver	Liver
25	chr5:50261800-50263400	Enhancers	Pancreas	Pancrea
26	chr5:50262000-50262600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr5:50262000-50262600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
28	chr5:50262000-50262600	Enhancers	Right Atrium	heart
29	chr5:50262000-50262800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr5:50262000-50262800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
31	chr5:50262000-50263200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
32	chr5:50262000-50263400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
33	chr5:50262000-50264000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:50262200-50262600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr5:50262200-50262600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:50262200-50262600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:50262200-50263200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:50262200-50263600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:50262200-50263800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr5:50262200-50264000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:50262200-50264200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr5:50262400-50262600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:50262400-50262600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
44	chr5:50262400-50262600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr5:50262400-50262600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
46	chr5:50262400-50262600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
47	chr5:50262400-50262600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
48	chr5:50262400-50262600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
49	chr5:50262400-50262600	Enhancers	Spleen	Spleen
50	chr5:50262400-50262800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion

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