Variant report

Variant	rs383902
Chromosome Location	chr15:59034174-59034175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59033413..59035094-chr15:59037580..59040574,2	MCF-7	breast:
2	chr15:59030650..59032606-chr15:59033863..59036396,2	K562	blood:
3	chr15:59033181..59035462-chr15:59039185..59042530,6	MCF-7	breast:
4	chr15:59033587..59035480-chr15:59035555..59037744,3	K562	blood:

Variant related genes	Relation type
ENSG00000137845	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10152558	0.91[CHB][hapmap]
rs11071398	0.88[CEU][hapmap];0.90[YRI][hapmap]
rs11638244	0.85[YRI][hapmap]
rs11854073	0.92[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12439457	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12899638	0.95[YRI][hapmap]
rs1427281	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs1427282	0.81[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs1648532	0.89[CHB][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17190727	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17269397	0.91[CHB][hapmap]
rs2250583	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2555356	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2657125	0.95[YRI][hapmap]
rs28864995	0.92[ASW][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap]
rs347115	0.83[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs347117	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs387812	0.88[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs395601	0.88[CEU][hapmap]
rs411007	0.84[CEU][hapmap];0.82[AFR][1000 genomes]
rs421829	0.86[AFR][1000 genomes]
rs442495	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs474875	0.83[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4774310	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4775086	0.83[GIH][hapmap]
rs4775087	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4775094	0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap]
rs507801	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs514049	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs585192	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs593742	0.84[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]
rs596379	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs605928	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs610877	0.83[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs640704	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6494029	1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs6494036	0.83[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs650366	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs653765	0.92[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs673813	0.89[CHB][hapmap];0.87[EUR][1000 genomes]
rs714696	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7161889	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7163162	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7171818	0.90[CHB][hapmap]
rs7177678	0.83[GIH][hapmap]
rs7183336	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs8043406	0.81[GIH][hapmap]
rs972801	0.92[ASW][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:59009800-59035400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:59016800-59034200	Weak transcription	Brain Germinal Matrix	brain
4	chr15:59017200-59034400	Weak transcription	Fetal Kidney	kidney
5	chr15:59022200-59040200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:59022600-59034800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:59022600-59038600	Weak transcription	Fetal Brain Female	brain
8	chr15:59023600-59040000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr15:59024000-59038200	Weak transcription	Fetal Stomach	stomach
10	chr15:59024200-59034600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:59024400-59035200	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:59024600-59034400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:59025600-59035200	Weak transcription	Psoas Muscle	Psoas
14	chr15:59025600-59038200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:59025600-59038200	Weak transcription	Gastric	stomach
16	chr15:59025600-59040000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:59025800-59034400	Weak transcription	HSMMtube	muscle
18	chr15:59025800-59034600	Weak transcription	Thymus	Thymus
19	chr15:59025800-59034600	Weak transcription	Spleen	Spleen
20	chr15:59025800-59034800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:59026800-59039600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:59027000-59035000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:59027000-59035200	Enhancers	Primary T cells from cord blood	blood
24	chr15:59027000-59039800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr15:59027200-59035000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:59027400-59034800	Weak transcription	Right Atrium	heart
27	chr15:59027600-59037800	Weak transcription	Fetal Intestine Small	intestine
28	chr15:59027600-59038000	Weak transcription	Fetal Intestine Large	intestine
29	chr15:59027600-59040200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr15:59029600-59034800	Enhancers	HepG2	liver
31	chr15:59030400-59034400	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:59030600-59037800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:59030800-59034600	Weak transcription	Fetal Heart	heart
34	chr15:59030800-59037800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:59030800-59038200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:59030800-59038400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:59030800-59039400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr15:59031000-59035000	Weak transcription	Osteobl	bone
39	chr15:59031000-59039200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:59031200-59034400	Weak transcription	Fetal Lung	lung
41	chr15:59031200-59034600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:59031200-59034600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:59031200-59037800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:59031200-59037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:59031400-59034200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:59031400-59034400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:59031400-59034600	Weak transcription	Small Intestine	intestine
48	chr15:59031400-59035800	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr15:59031400-59037800	Weak transcription	Hela-S3	cervix
50	chr15:59031400-59037800	Weak transcription	NHEK	skin

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