Variant report

Variant	rs10838530
Chromosome Location	chr11:45942995-45942996
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	SIN3A	chr11:45942868-45945276	H1-hESC	embryonic stem cell:	n/a	chr11:45944228-45944241 chr11:45944150-45944161 chr11:45943644-45943653 chr11:45943637-45943650
2	NFIC	chr11:45942901-45944220	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr11:45942936-45944627	ECC-1	luminal epithelium:	n/a	chr11:45943840-45943850
4	GATA3	chr11:45942945-45944049	T-47D	breast:	n/a	n/a
5	FOXA1	chr11:45942966-45943274	T-47D	breast:	n/a	n/a
6	CTBP2	chr11:45942964-45944255	H1-hESC	embryonic stem cell:	n/a	n/a
7	EP300	chr11:45942781-45944534	ECC-1	luminal epithelium:	n/a	chr11:45942994-45943001 chr11:45944326-45944342 chr11:45944234-45944250 chr11:45943936-45943952
8	POLR2A	chr11:45942718-45945382	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr11:45942907-45943400	ECC-1	luminal epithelium:	n/a	n/a
10	ZBTB7A	chr11:45942756-45944675	ECC-1	luminal epithelium:	n/a	chr11:45944107-45944114 chr11:45944141-45944148
11	POLR2A	chr11:45942932-45943960	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF12	chr11:45942880-45944600	ECC-1	luminal epithelium:	n/a	chr11:45944386-45944396
13	TEAD4	chr11:45942760-45944448	ECC-1	luminal epithelium:	n/a	n/a
14	STAT3	chr11:45942941-45943038	MCF10A-Er-Src	breast:	n/a	n/a
15	ZBTB7A	chr11:45942892-45944794	ECC-1	luminal epithelium:	n/a	chr11:45944107-45944114 chr11:45944141-45944148
16	TCF12	chr11:45942778-45944432	ECC-1	luminal epithelium:	n/a	chr11:45944386-45944396
17	NFIC	chr11:45942917-45944445	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:45867151..45870859-chr11:45942545..45946514,4	K562	blood:
2	chr11:45942684..45944705-chr11:46141351..46143147,2	K562	blood:
3	chr11:45879680..45881437-chr11:45942342..45944046,2	MCF-7	breast:
4	chr11:45942020..45943576-chr11:46141975..46144467,2	MCF-7	breast:

Variant related genes	Relation type
PEX16	TF binding region
GYLTL1B	TF binding region
ENSG00000135365	Chromatin interaction
ENSG00000121671	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10838531	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1132349	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11600112	0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs2271847	0.82[JPT][hapmap]
rs2280331	0.85[JPT][hapmap]
rs3802758	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7109981	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7115790	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7124323	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7124434	0.88[AMR][1000 genomes]
rs7925824	0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs867813	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs939108	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1047462	chr11:45898630-45953696	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking 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 target site	14 gene(s)	inside rSNPs	diseases
3	nsv516442	chr11:45899962-45983385	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
4	esv1794798	chr11:45903280-45953636	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv1805505	chr11:45912324-45956109	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv1798496	chr11:45925495-45948304	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3327833	chr11:45942401-45945249	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45940400-45943000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:45940400-45943400	Weak transcription	Fetal Heart	heart
3	chr11:45940400-45943600	Weak transcription	Lung	lung
4	chr11:45940400-45943800	Weak transcription	Aorta	Aorta
5	chr11:45940600-45943000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:45940600-45943000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:45940600-45943000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:45940600-45943200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr11:45940600-45943200	Weak transcription	Ovary	ovary
10	chr11:45940600-45943400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:45940600-45943400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:45940600-45943400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:45940600-45943400	Weak transcription	HMEC	breast
14	chr11:45940600-45943600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr11:45940600-45943600	Enhancers	Brain Substantia Nigra	brain
16	chr11:45940600-45943600	Enhancers	K562	blood
17	chr11:45940600-45943600	Weak transcription	NHEK	skin
18	chr11:45940800-45943200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:45941000-45943400	Enhancers	Primary B cells from cord blood	blood
20	chr11:45941000-45943400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr11:45941000-45943400	Weak transcription	Liver	Liver
22	chr11:45941000-45943600	Enhancers	Primary B cells from peripheral blood	blood
23	chr11:45941000-45943600	Weak transcription	Right Ventricle	heart
24	chr11:45941000-45943800	Weak transcription	Right Atrium	heart
25	chr11:45941200-45943000	Weak transcription	Gastric	stomach
26	chr11:45941200-45943400	Weak transcription	Left Ventricle	heart
27	chr11:45941200-45943400	Weak transcription	Spleen	Spleen
28	chr11:45941200-45943600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:45941200-45944000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr11:45941200-45953400	Weak transcription	Dnd41	blood
31	chr11:45941600-45943000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:45941600-45943000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr11:45941600-45943000	Enhancers	Brain Anterior Caudate	brain
34	chr11:45941600-45943000	Enhancers	Placenta	Placenta
35	chr11:45941600-45943200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:45941600-45943200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:45941600-45943400	Enhancers	Pancreas	Pancrea
38	chr11:45941800-45943000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr11:45941800-45943200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr11:45941800-45943400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:45941800-45943400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:45942000-45943000	Enhancers	H9 Cell Line	embryonic stem cell
43	chr11:45942000-45943000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
44	chr11:45942000-45943200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:45942000-45943200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:45942000-45943200	Weak transcription	Esophagus	oesophagus
47	chr11:45942000-45943400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:45942000-45943400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr11:45942000-45943400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:45942200-45943000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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