Variant report

Variant	rs2554330
Chromosome Location	chr15:52156931-52156932
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	SIN3AK20	chr15:52156481-52157083	HCT-116	colon:	n/a	n/a
2	FOS	chr15:52156526-52157056	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr15:52156527-52157047	MCF10A-Er-Src	breast:	n/a	n/a
4	SP1	chr15:52156429-52157181	HCT-116	colon:	n/a	n/a
5	TCF7L2	chr15:52156710-52156967	MCF-7	breast:	n/a	n/a
6	SP1	chr15:52156420-52157296	HCT-116	colon:	n/a	n/a
7	CBX3	chr15:52156507-52157132	HCT-116	colon:	n/a	n/a
8	JUND	chr15:52156358-52157195	HCT-116	colon:	n/a	n/a
9	FOS	chr15:52156495-52157058	MCF10A-Er-Src	breast:	n/a	n/a
10	JUND	chr15:52156423-52157178	HCT-116	colon:	n/a	n/a
11	CBX3	chr15:52156411-52157163	HCT-116	colon:	n/a	n/a
12	TCF7L2	chr15:52156625-52157012	HCT-116	colon:	n/a	n/a
13	STAT3	chr15:52156493-52156932	MCF10A-Er-Src	breast:	n/a	n/a
14	MAX	chr15:52156484-52157190	HCT-116	colon:	n/a	n/a
15	POLR2A	chr15:52156558-52157039	HCT-116	colon:	n/a	n/a
16	RUNX3	chr15:52156677-52156955	GM12878	blood:	n/a	n/a
17	STAT3	chr15:52156518-52157038	MCF10A-Er-Src	breast:	n/a	n/a
18	TEAD4	chr15:52156468-52157131	HCT-116	colon:	n/a	n/a
19	SRF	chr15:52156581-52157216	HCT-116	colon:	n/a	n/a
20	FOS	chr15:52156518-52157057	MCF10A-Er-Src	breast:	n/a	n/a
21	MYC	chr15:52156536-52157038	MCF10A-Er-Src	breast:	n/a	n/a
22	NR3C1	chr15:52156490-52156968	A549	lung:	n/a	n/a
23	STAT3	chr15:52156514-52157001	MCF10A-Er-Src	breast:	n/a	n/a
24	ZBTB33	chr15:52156581-52157083	HCT-116	colon:	n/a	n/a
25	REST	chr15:52156601-52157162	MCF-7	breast:	n/a	n/a
26	FOSL1	chr15:52156432-52157181	HCT-116	colon:	n/a	n/a
27	FOSL1	chr15:52156352-52157264	HCT-116	colon:	n/a	n/a
28	MAX	chr15:52156466-52157150	HCT-116	colon:	n/a	n/a
29	STAT3	chr15:52156610-52156972	MCF10A-Er-Src	breast:	n/a	n/a
30	MYC	chr15:52156554-52156993	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52151375..52154020-chr15:52156501..52159080,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259632	TF binding region
ENSG00000259632	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1025185	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10519323	1.00[EUR][1000 genomes]
rs10519325	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519326	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438469	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442283	1.00[EUR][1000 genomes]
rs1378891	1.00[EUR][1000 genomes]
rs1426085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1426086	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649047	1.00[EUR][1000 genomes]
rs17649178	1.00[EUR][1000 genomes]
rs17649255	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649391	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649692	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17649801	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17705530	1.00[EUR][1000 genomes]
rs17705649	1.00[EUR][1000 genomes]
rs17705685	1.00[EUR][1000 genomes]
rs17705889	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17706076	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2052707	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2162224	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2263946	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2436663	0.85[AFR][1000 genomes]
rs2436664	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470609	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2470613	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554309	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554310	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554311	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554317	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2554318	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554321	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2554323	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554324	0.85[AFR][1000 genomes]
rs2554325	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554326	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554329	0.85[AFR][1000 genomes]
rs2554333	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554341	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554344	0.85[AFR][1000 genomes]
rs2554351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554352	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554356	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570218	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570219	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570220	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570221	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570225	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2570227	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570232	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2570234	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570242	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570244	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2570245	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570246	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2570247	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570257	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570259	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570261	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570262	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2570267	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570270	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570273	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2570274	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2593165	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2593175	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2593176	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2593180	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623248	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2623250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623252	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623253	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623257	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623260	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623261	0.95[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2623264	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623267	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623268	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623273	0.85[AFR][1000 genomes]
rs2623274	0.85[AFR][1000 genomes]
rs2623275	0.85[AFR][1000 genomes]
rs2623277	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623278	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623287	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623293	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2899483	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2916174	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2959297	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959303	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099570	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34407523	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3794533	1.00[EUR][1000 genomes]
rs3794537	1.00[EUR][1000 genomes]
rs4774600	1.00[EUR][1000 genomes]
rs4774601	1.00[EUR][1000 genomes]
rs4775979	1.00[EUR][1000 genomes]
rs4775987	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775988	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775989	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7166322	1.00[EUR][1000 genomes]
rs7170429	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7170700	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7173661	1.00[EUR][1000 genomes]
rs7179139	1.00[EUR][1000 genomes]
rs73411105	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74013606	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8024441	1.00[EUR][1000 genomes]
rs8026507	1.00[EUR][1000 genomes]
rs8027426	1.00[EUR][1000 genomes]
rs8042310	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs919056	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs919057	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919058	0.85[AFR][1000 genomes]
rs990666	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52141600-52166800	Weak transcription	Stomach Mucosa	stomach
2	chr15:52141800-52176200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:52145800-52176600	Weak transcription	Psoas Muscle	Psoas
4	chr15:52148200-52157000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:52148200-52176200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:52149000-52161000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:52149400-52171000	Weak transcription	Brain Angular Gyrus	brain
8	chr15:52149800-52160600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:52149800-52168000	Weak transcription	Right Ventricle	heart
10	chr15:52150600-52160800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:52152400-52170000	Weak transcription	Pancreas	Pancrea
12	chr15:52152400-52170800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:52153200-52158400	Genic enhancers	A549	lung
14	chr15:52153200-52161200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:52153200-52161600	Genic enhancers	NHEK	skin
16	chr15:52153400-52157000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:52153400-52158400	Strong transcription	Hela-S3	cervix
18	chr15:52153400-52161600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:52153800-52158000	Strong transcription	GM12878-XiMat	blood
20	chr15:52153800-52178000	Weak transcription	Brain Germinal Matrix	brain
21	chr15:52154000-52161600	Genic enhancers	HMEC	breast
22	chr15:52154400-52159400	Weak transcription	Fetal Heart	heart
23	chr15:52154400-52162000	Weak transcription	Small Intestine	intestine
24	chr15:52154400-52165800	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:52154400-52170200	Weak transcription	Fetal Brain Male	brain
26	chr15:52154800-52158000	Strong transcription	NHLF	lung
27	chr15:52155000-52157000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:52155000-52157200	Strong transcription	Fetal Lung	lung
29	chr15:52155000-52157200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:52155000-52157400	Strong transcription	Brain Hippocampus Middle	brain
31	chr15:52155000-52157400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr15:52155000-52157400	Strong transcription	Placenta	Placenta
33	chr15:52155000-52157600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr15:52155000-52157600	Strong transcription	K562	blood
35	chr15:52155000-52157800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr15:52155000-52157800	Strong transcription	Fetal Muscle Leg	muscle
37	chr15:52155000-52158000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:52155000-52158000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:52155000-52158000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:52155000-52158000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:52155000-52158000	Strong transcription	Adipose Nuclei	Adipose
42	chr15:52155000-52158000	Strong transcription	HSMM	muscle
43	chr15:52155000-52158000	Strong transcription	HUVEC	blood vessel
44	chr15:52155000-52158800	Strong transcription	Fetal Intestine Large	intestine
45	chr15:52155000-52160000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:52155000-52160400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr15:52155000-52160800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr15:52155000-52162600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:52155000-52162800	Strong transcription	Fetal Stomach	stomach
50	chr15:52155000-52164000	Strong transcription	Primary B cells from cord blood	blood

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