Variant report

Variant	rs2593213
Chromosome Location	chr15:57410215-57410216
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	GATA3	chr15:57409948-57410722	SK-N-SH	brain:	n/a	chr15:57410182-57410203 chr15:57410222-57410238 chr15:57410185-57410196
2	EP300	chr15:57410104-57410555	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr15:57410152-57410530	SK-N-SH_RA	brain:	n/a	n/a
4	STAT3	chr15:57410009-57410350	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA3	chr15:57410014-57410405	SH-SY5Y	brain:	n/a	chr15:57410182-57410203 chr15:57410222-57410238 chr15:57410185-57410196
6	RFX5	chr15:57410126-57410629	Hela-S3	cervix:	n/a	n/a
7	GATA3	chr15:57409861-57410662	SK-N-SH	brain:	n/a	chr15:57410182-57410203 chr15:57410222-57410238 chr15:57410185-57410196
8	GATA2	chr15:57410178-57410399	SH-SY5Y	brain:	n/a	chr15:57410182-57410203 chr15:57410222-57410238 chr15:57410185-57410196
9	FOXA1	chr15:57410193-57410620	HepG2	liver:	n/a	n/a
10	FOSL2	chr15:57410148-57410697	A549	lung:	n/a	chr15:57410173-57410181 chr15:57410472-57410484 chr15:57410174-57410181
11	FOS	chr15:57410198-57410692	HUVEC	blood vessel:	n/a	chr15:57410467-57410478 chr15:57410472-57410484
12	GATA2	chr15:57410089-57410503	HUVEC	blood vessel:	n/a	chr15:57410182-57410203 chr15:57410222-57410238 chr15:57410185-57410196
13	PBX3	chr15:57410111-57410588	SK-N-SH	brain:	n/a	n/a
14	FOXA1	chr15:57410174-57410517	HepG2	liver:	n/a	n/a
15	JUND	chr15:57410146-57410699	SK-N-SH	brain:	n/a	chr15:57410173-57410181 chr15:57410467-57410478 chr15:57410472-57410484 chr15:57410174-57410181

Variant related genes	Relation type
TCF12	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1652733	1.00[YRI][hapmap]
rs213154	1.00[YRI][hapmap]
rs2243575	0.93[AFR][1000 genomes]
rs2431022	1.00[YRI][hapmap]
rs2431031	1.00[YRI][hapmap]
rs2435900	1.00[YRI][hapmap]
rs2435901	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2435902	1.00[YRI][hapmap]
rs2435904	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2439923	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2566839	1.00[YRI][hapmap]
rs2566841	1.00[YRI][hapmap]
rs2566847	0.87[AFR][1000 genomes]
rs2566852	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2585085	0.93[AFR][1000 genomes]
rs2585092	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2585095	0.93[AFR][1000 genomes]
rs2585096	1.00[YRI][hapmap]
rs2585098	1.00[YRI][hapmap]
rs2585101	0.93[AFR][1000 genomes]
rs2585109	0.87[AFR][1000 genomes]
rs2585111	0.81[AFR][1000 genomes]
rs2591067	1.00[YRI][hapmap]
rs2593214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593227	0.81[AFR][1000 genomes]
rs2615219	1.00[YRI][hapmap]
rs2615234	0.93[AFR][1000 genomes]
rs2703603	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2703606	0.81[AFR][1000 genomes]
rs2703609	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2703615	1.00[YRI][hapmap]
rs2703622	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2703625	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733169	0.87[AFR][1000 genomes]
rs2733173	0.81[AFR][1000 genomes]
rs2733175	0.87[AFR][1000 genomes]
rs2733186	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2733190	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2733196	1.00[YRI][hapmap]
rs2733301	1.00[YRI][hapmap]
rs2733308	0.87[AFR][1000 genomes]
rs2733319	1.00[YRI][hapmap]
rs2733325	1.00[AMR][1000 genomes]
rs2733344	1.00[YRI][hapmap]
rs2920271	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs8042069	1.00[YRI][hapmap]

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	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
2	chr15:57381000-57412400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:57382800-57419600	Weak transcription	K562	blood
5	chr15:57384600-57410400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
9	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
11	chr15:57397800-57416600	Weak transcription	Fetal Stomach	stomach
12	chr15:57398000-57415800	Weak transcription	Fetal Intestine Small	intestine
13	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:57399600-57416200	Weak transcription	Primary T cells from cord blood	blood
15	chr15:57402600-57414600	Weak transcription	Primary B cells from cord blood	blood
16	chr15:57403000-57424600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:57403800-57425200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:57404600-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:57404800-57411200	Weak transcription	Spleen	Spleen
20	chr15:57404800-57415600	Weak transcription	Thymus	Thymus
21	chr15:57406000-57410600	Enhancers	Duodenum Mucosa	Duodenum
22	chr15:57406800-57413000	Weak transcription	Gastric	stomach
23	chr15:57406800-57413000	Weak transcription	Left Ventricle	heart
24	chr15:57406800-57413000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:57406800-57414200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr15:57406800-57414600	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:57406800-57416200	Weak transcription	Fetal Muscle Leg	muscle
28	chr15:57406800-57425000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:57406800-57425400	Weak transcription	Pancreas	Pancrea
30	chr15:57406800-57425600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:57406800-57425600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr15:57406800-57426400	Weak transcription	Colonic Mucosa	Colon
33	chr15:57406800-57426600	Weak transcription	Psoas Muscle	Psoas
34	chr15:57407000-57413600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:57407400-57412600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr15:57407400-57413200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:57407600-57425600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:57408000-57411000	Enhancers	Brain Anterior Caudate	brain
39	chr15:57408200-57412800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr15:57408200-57413200	Weak transcription	Small Intestine	intestine
41	chr15:57408400-57414400	Weak transcription	Stomach Mucosa	stomach
42	chr15:57408800-57410600	Enhancers	Liver	Liver
43	chr15:57409200-57410400	Enhancers	Brain Cingulate Gyrus	brain
44	chr15:57409200-57410600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:57409200-57411000	Enhancers	Brain Germinal Matrix	brain
46	chr15:57409200-57411000	Enhancers	HUVEC	blood vessel
47	chr15:57409200-57411200	Enhancers	Fetal Brain Male	brain
48	chr15:57409200-57414000	Enhancers	Brain Substantia Nigra	brain
49	chr15:57409400-57410800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr15:57409400-57411000	Enhancers	NHLF	lung

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