Variant report

Variant	rs7984159
Chromosome Location	chr13:80057839-80057840
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	FOS	chr13:80057609-80057875	MCF10A-Er-Src	breast:	n/a	chr13:80057704-80057714 chr13:80057704-80057714 chr13:80057704-80057714
2	POLR2A	chr13:80054410-80058154	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr13:80057481-80058200	MCF10A-Er-Src	breast:	n/a	chr13:80058028-80058036 chr13:80058026-80058037
4	POLR2A	chr13:80057467-80057853	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr13:80057294-80058206	MCF10A-Er-Src	breast:	n/a	chr13:80058028-80058036 chr13:80058026-80058037
6	POLR2A	chr13:80057124-80057873	K562	blood:	n/a	n/a
7	CEBPB	chr13:80057266-80057945	IMR90	lung:	n/a	chr13:80057440-80057451
8	STAT3	chr13:80057355-80058206	MCF10A-Er-Src	breast:	n/a	chr13:80058028-80058036 chr13:80058026-80058037
9	POLR2A	chr13:80054586-80058161	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr13:80057366-80058197	MCF10A-Er-Src	breast:	n/a	chr13:80058028-80058036 chr13:80058026-80058037
11	FOS	chr13:80057458-80058196	MCF10A-Er-Src	breast:	n/a	chr13:80057704-80057714 chr13:80057704-80057714 chr13:80057704-80057714
12	FOS	chr13:80057416-80058126	MCF10A-Er-Src	breast:	n/a	chr13:80057704-80057714 chr13:80057704-80057714 chr13:80057704-80057714

No.	Distal block	Cell Line	Cell type
1	chr13:80054400..80056939-chr13:80057406..80059171,2	MCF-7	breast:
2	chr13:80057193..80059999-chr13:80114272..80116741,2	K562	blood:
3	chr13:80056153..80058862-chr13:80062367..80066425,4	K562	blood:

Variant related genes	Relation type
NDFIP2-AS1	TF binding region
ENSG00000232132	Chromatin interaction
ENSG00000102471	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10492579	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10507899	0.92[EUR][1000 genomes]
rs1335372	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1335373	0.84[EUR][1000 genomes]
rs1335374	0.80[EUR][1000 genomes]
rs1414157	0.92[EUR][1000 genomes]
rs17071385	0.80[EUR][1000 genomes]
rs17071415	0.80[EUR][1000 genomes]
rs17071499	1.00[EUR][1000 genomes]
rs17071532	0.92[EUR][1000 genomes]
rs17071549	0.88[EUR][1000 genomes]
rs17071558	0.85[EUR][1000 genomes]
rs17071566	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17071574	0.92[EUR][1000 genomes]
rs17071585	0.92[EUR][1000 genomes]
rs17071627	0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17071632	0.84[EUR][1000 genomes]
rs41288268	1.00[EUR][1000 genomes]
rs56711390	0.92[EUR][1000 genomes]
rs57032852	0.92[EUR][1000 genomes]
rs57544957	0.80[EUR][1000 genomes]
rs57929179	0.88[EUR][1000 genomes]
rs58056613	0.96[EUR][1000 genomes]
rs58069884	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58264675	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58406632	0.92[EUR][1000 genomes]
rs59165380	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59381369	0.84[EUR][1000 genomes]
rs59755477	0.88[EUR][1000 genomes]
rs59773478	0.80[EUR][1000 genomes]
rs59783325	0.92[EUR][1000 genomes]
rs60126328	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61318325	0.88[EUR][1000 genomes]
rs61676417	0.92[EUR][1000 genomes]
rs6563107	0.80[EUR][1000 genomes]
rs6563117	0.92[EUR][1000 genomes]
rs7139902	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7317409	0.84[EUR][1000 genomes]
rs7317511	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7318854	0.84[EUR][1000 genomes]
rs7318984	0.84[EUR][1000 genomes]
rs7327148	0.92[EUR][1000 genomes]
rs7329633	0.92[EUR][1000 genomes]
rs7330804	0.84[EUR][1000 genomes]
rs7335191	0.80[EUR][1000 genomes]
rs7338043	0.92[EUR][1000 genomes]
rs73548948	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73548951	1.00[EUR][1000 genomes]
rs73548955	1.00[EUR][1000 genomes]
rs73551558	1.00[EUR][1000 genomes]
rs73551595	0.92[EUR][1000 genomes]
rs73551596	0.92[EUR][1000 genomes]
rs73551597	0.92[EUR][1000 genomes]
rs73551601	0.92[EUR][1000 genomes]
rs73551602	0.92[EUR][1000 genomes]
rs73553403	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73553418	0.88[EUR][1000 genomes]
rs73553424	0.92[EUR][1000 genomes]
rs73553431	0.92[EUR][1000 genomes]
rs73553447	0.92[EUR][1000 genomes]
rs73553448	0.88[EUR][1000 genomes]
rs73553473	0.92[EUR][1000 genomes]
rs73553481	0.88[EUR][1000 genomes]
rs73553499	0.84[EUR][1000 genomes]
rs73555409	0.80[EUR][1000 genomes]
rs73555411	0.84[EUR][1000 genomes]
rs73555415	0.84[EUR][1000 genomes]
rs73566422	0.80[EUR][1000 genomes]
rs73566424	0.80[EUR][1000 genomes]
rs73566435	0.80[EUR][1000 genomes]
rs73566454	0.80[EUR][1000 genomes]
rs7491258	0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7981574	0.92[EUR][1000 genomes]
rs7984598	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7985220	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7985697	1.00[EUR][1000 genomes]
rs7990190	0.92[EUR][1000 genomes]
rs7990464	0.92[EUR][1000 genomes]
rs7992181	0.80[EUR][1000 genomes]
rs7997554	0.96[EUR][1000 genomes]
rs7998452	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8000870	1.00[EUR][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	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80054800-80058000	Active TSS	Duodenum Mucosa	Duodenum
2	chr13:80054800-80059400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr13:80056000-80058800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:80056200-80058000	Enhancers	Stomach Mucosa	stomach
5	chr13:80056200-80058000	Flanking Active TSS	NH-A	brain
6	chr13:80056200-80058800	Weak transcription	Small Intestine	intestine
7	chr13:80056200-80059200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:80056200-80060600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr13:80056200-80060800	Weak transcription	Gastric	stomach
10	chr13:80056200-80063200	Weak transcription	Left Ventricle	heart
11	chr13:80056200-80066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr13:80056200-80066600	Weak transcription	Psoas Muscle	Psoas
13	chr13:80056200-80077400	Weak transcription	Right Ventricle	heart
14	chr13:80056400-80058000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:80056400-80058000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr13:80056400-80058000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr13:80056600-80058000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr13:80056600-80058000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:80056600-80058000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr13:80056600-80058600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr13:80056600-80064200	Weak transcription	Placenta	Placenta
22	chr13:80056800-80058000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr13:80056800-80058000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:80056800-80058000	Enhancers	Brain Cingulate Gyrus	brain
25	chr13:80056800-80058000	Flanking Active TSS	NHDF-Ad	bronchial
26	chr13:80056800-80058800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr13:80056800-80059200	Weak transcription	Pancreas	Pancrea
28	chr13:80056800-80059600	Enhancers	Brain Hippocampus Middle	brain
29	chr13:80056800-80059600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr13:80056800-80061200	Enhancers	Fetal Heart	heart
31	chr13:80056800-80064000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr13:80056800-80064400	Weak transcription	Fetal Stomach	stomach
33	chr13:80056800-80065800	Weak transcription	Fetal Muscle Leg	muscle
34	chr13:80057000-80058000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr13:80057000-80058000	Flanking Active TSS	Osteobl	bone
36	chr13:80057000-80058400	Enhancers	K562	blood
37	chr13:80057000-80058800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:80057000-80058800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr13:80057000-80058800	Enhancers	Liver	Liver
40	chr13:80057000-80059000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr13:80057000-80059200	Enhancers	HepG2	liver
42	chr13:80057000-80063600	Weak transcription	Right Atrium	heart
43	chr13:80057000-80066200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr13:80057200-80058000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr13:80057200-80058000	Flanking Active TSS	A549	lung
46	chr13:80057200-80058000	Flanking Active TSS	HMEC	breast
47	chr13:80057200-80058400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr13:80057200-80058400	Flanking Active TSS	Dnd41	blood
49	chr13:80057200-80059200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr13:80057200-80060600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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