Variant report

Variant	rs11039519
Chromosome Location	chr11:48130094-48130095
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:48125100..48126917-chr11:48129444..48131504,2	MCF-7	breast:
2	chr11:47999992..48004999-chr11:48128626..48133853,5	MCF-7	breast:
3	chr11:47967425..47969925-chr11:48129768..48132712,2	MCF-7	breast:
4	chr11:48120614..48123449-chr11:48129423..48131714,2	MCF-7	breast:
5	chr11:48129232..48130878-chr11:48134176..48136053,2	K562	blood:
6	chr11:48068073..48069888-chr11:48129032..48131534,2	MCF-7	breast:
7	chr11:48036717..48039459-chr11:48129718..48132138,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149177	Chromatin interaction
ENSG00000254879	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10734562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742828	0.90[EUR][1000 genomes]
rs10742829	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10742831	1.00[ASN][1000 genomes]
rs10742834	0.82[EUR][1000 genomes]
rs10742836	0.82[EUR][1000 genomes]
rs10769316	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769317	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838805	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039515	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039520	0.85[ASN][1000 genomes]
rs11039538	0.81[ASN][1000 genomes]
rs11603850	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1503171	0.82[EUR][1000 genomes]
rs1503188	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503190	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1532754	1.00[ASN][1000 genomes]
rs1875696	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910364	1.00[ASN][1000 genomes]
rs1969093	1.00[ASN][1000 genomes]
rs2174129	0.90[EUR][1000 genomes]
rs2270993	0.85[ASN][1000 genomes]
rs2279822	0.85[ASN][1000 genomes]
rs2279823	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3942852	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4597030	0.82[EUR][1000 genomes]
rs4752806	1.00[ASN][1000 genomes]
rs4752807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752808	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752893	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752897	1.00[ASN][1000 genomes]
rs4752900	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4752901	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6485806	0.90[EUR][1000 genomes]
rs6485809	0.98[ASN][1000 genomes]
rs7113857	0.85[ASN][1000 genomes]
rs7117386	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7129364	0.83[ASN][1000 genomes]
rs905475	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs905477	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
15	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv897329	chr11:48052676-48319974	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv1048554	chr11:48062861-48388686	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
18	nsv1038210	chr11:48068862-48388686	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
19	nsv1052076	chr11:48077864-48702549	ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
20	nsv869354	chr11:48088580-48783113	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
21	nsv1045734	chr11:48089315-48893207	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
22	nsv467871	chr11:48106486-48694871	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
23	nsv554211	chr11:48106486-48694871	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
24	nsv948502	chr11:48110043-48891877	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
25	nsv1050815	chr11:48126145-48342923	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
26	nsv1043509	chr11:48127618-48616507	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
27	nsv541039	chr11:48127618-48616507	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
28	nsv1049379	chr11:48129034-48374636	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48114600-48131400	Weak transcription	Esophagus	oesophagus
2	chr11:48116600-48131200	Weak transcription	Psoas Muscle	Psoas
3	chr11:48118800-48131200	Weak transcription	Ovary	ovary
4	chr11:48119600-48131400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:48122800-48130600	Enhancers	Spleen	Spleen
6	chr11:48123200-48131200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:48123400-48130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:48123400-48131200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr11:48123600-48131200	Enhancers	Liver	Liver
10	chr11:48124000-48131200	Weak transcription	Fetal Lung	lung
11	chr11:48124200-48131200	Enhancers	Primary B cells from peripheral blood	blood
12	chr11:48125400-48131200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:48125600-48132200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr11:48125800-48130400	Weak transcription	Small Intestine	intestine
15	chr11:48125800-48130800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr11:48125800-48131200	Weak transcription	Aorta	Aorta
17	chr11:48125800-48131600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:48126000-48130200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:48126000-48130800	Weak transcription	Fetal Brain Male	brain
20	chr11:48126000-48131000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:48126000-48131200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr11:48126000-48131200	Weak transcription	NHEK	skin
23	chr11:48126200-48131200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:48126200-48132000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr11:48126400-48130200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:48126400-48130800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:48126400-48131000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:48126400-48131200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:48126400-48131200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:48126400-48131200	Enhancers	Brain Hippocampus Middle	brain
31	chr11:48126400-48131200	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:48126400-48131200	Weak transcription	Stomach Mucosa	stomach
33	chr11:48126400-48131600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:48126400-48147400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:48126600-48130400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:48126600-48130400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:48126600-48130800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr11:48126600-48131200	Weak transcription	Fetal Heart	heart
39	chr11:48126600-48131200	Weak transcription	Right Ventricle	heart
40	chr11:48126600-48131200	Weak transcription	HepG2	liver
41	chr11:48126600-48136000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:48126800-48130200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:48126800-48131000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr11:48126800-48131200	Enhancers	Primary T cells fromperipheralblood	blood
45	chr11:48126800-48131200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr11:48126800-48131200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:48126800-48131200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:48127000-48130400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:48127000-48130600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:48127000-48131200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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