Variant report

Variant	rs11630924
Chromosome Location	chr15:74496293-74496294
allele	C/G
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	BACH1	chr15:74496082-74496694	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFK	chr15:74496197-74496644	H1-hESC	embryonic stem cell:	n/a	chr15:74496475-74496491 chr15:74496480-74496489
3	POLR2A	chr15:74496148-74496608	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr15:74496276-74496565	K562	blood:	n/a	n/a
5	RAD21	chr15:74496188-74496678	H1-hESC	embryonic stem cell:	n/a	chr15:74496433-74496445
6	NFIC	chr15:74496087-74496612	GM12878	blood:	n/a	n/a
7	CTCF	chr15:74496260-74496410	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:74496147-74496775	SK-N-MC	brain:	n/a	n/a
9	RAD21	chr15:74496196-74496840	SK-N-SH_RA	brain:	n/a	chr15:74496802-74496815 chr15:74496433-74496445
10	RAD21	chr15:74496205-74496565	H1-hESC	embryonic stem cell:	n/a	chr15:74496433-74496445
11	ZNF263	chr15:74494807-74496849	HEK293-T-REx	kidney:	n/a	chr15:74495716-74495725 chr15:74495068-74495077 chr15:74495251-74495260
12	TBP	chr15:74496280-74496517	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr15:74496280-74496430	AG04450	lung:	n/a	n/a
14	EP300	chr15:74496286-74496818	SK-N-SH_RA	brain:	n/a	chr15:74496511-74496519 chr15:74496747-74496763
15	EP300	chr15:74496188-74496743	SK-N-SH_RA	brain:	n/a	chr15:74496511-74496519
16	CTCF	chr15:74496280-74496430	SK-N-SH_RA	brain:	n/a	n/a
17	POLR2A	chr15:74496248-74496775	SK-N-SH	brain:	n/a	n/a
18	MAZ	chr15:74496217-74496973	IMR90	lung:	n/a	n/a
19	POLR2A	chr15:74496178-74496650	SK-N-MC	brain:	n/a	n/a
20	SIN3A	chr15:74496237-74496486	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74419604..74420502-chr15:74495753..74496632,3	MCF-7	breast:
2	chr15:74495756..74498011-chr15:74498578..74500648,2	K562	blood:
3	chr15:74489184..74491442-chr15:74495568..74497527,4	MCF-7	breast:
4	chr15:74495538..74499115-chr15:74503082..74506667,3	MCF-7	breast:
5	chr15:74481853..74488513-chr15:74489689..74497281,13	MCF-7	breast:
6	chr15:74494443..74497074-chr15:74501503..74504271,2	K562	blood:
7	chr15:74494408..74497236-chr15:74500706..74502894,2	MCF-7	breast:

Variant related genes	Relation type
STRA6	TF binding region
ENSG00000137868	Chromatin interaction
ENSG00000167178	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11630317	0.85[EUR][1000 genomes]
rs11631509	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11631944	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs11633687	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11639090	0.88[EUR][1000 genomes]
rs11639369	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11854957	0.88[EUR][1000 genomes]
rs11857410	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12899173	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12905521	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907503	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911581	0.82[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912258	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12912578	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs12913041	0.89[EUR][1000 genomes]
rs12915891	0.83[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13259	0.88[EUR][1000 genomes]
rs2062309	0.86[EUR][1000 genomes]
rs2415169	0.88[EUR][1000 genomes]
rs2899824	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs34004794	0.81[AMR][1000 genomes]
rs34147822	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34234753	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34573746	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591452	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34868798	0.88[EUR][1000 genomes]
rs34985083	0.81[AMR][1000 genomes]
rs35036456	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35255788	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35462746	0.87[EUR][1000 genomes]
rs35661273	0.88[EUR][1000 genomes]
rs35917667	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3848160	0.88[EUR][1000 genomes]
rs3848161	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs3888004	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs409856	0.90[EUR][1000 genomes]
rs62003660	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62003661	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62005707	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62005709	0.88[EUR][1000 genomes]
rs62005710	0.88[EUR][1000 genomes]
rs62005711	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71399778	0.88[EUR][1000 genomes]
rs72747610	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs733163	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8037531	0.87[EUR][1000 genomes]
rs923118	0.88[EUR][1000 genomes]
rs9630417	0.86[EUR][1000 genomes]
rs971755	0.91[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs971756	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs971757	0.91[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][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	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74489200-74509600	Weak transcription	Gastric	stomach
2	chr15:74489400-74499000	Weak transcription	Brain Anterior Caudate	brain
3	chr15:74491000-74503200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:74492000-74496800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr15:74492600-74496400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:74492600-74496400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr15:74492600-74496600	Enhancers	HMEC	breast
8	chr15:74492600-74496800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:74492600-74497000	Enhancers	Ovary	ovary
10	chr15:74492600-74497000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr15:74492600-74497400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:74492600-74497800	Enhancers	GM12878-XiMat	blood
13	chr15:74492600-74498000	Enhancers	Fetal Lung	lung
14	chr15:74492600-74503200	Enhancers	Fetal Muscle Leg	muscle
15	chr15:74492800-74496600	Enhancers	Fetal Heart	heart
16	chr15:74493000-74496800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr15:74493200-74496800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:74493400-74496800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr15:74493400-74498000	Enhancers	NH-A	brain
20	chr15:74494000-74496400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:74494000-74497400	Weak transcription	Left Ventricle	heart
22	chr15:74494000-74498400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:74494000-74500200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr15:74494200-74501000	Weak transcription	HSMM	muscle
25	chr15:74494400-74497400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:74494400-74498400	Enhancers	Primary hematopoietic stem cells	blood
27	chr15:74494400-74500200	Enhancers	Fetal Brain Male	brain
28	chr15:74494600-74496600	Weak transcription	Esophagus	oesophagus
29	chr15:74494600-74496800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr15:74494600-74496800	Weak transcription	Spleen	Spleen
31	chr15:74494600-74498400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:74494800-74496800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:74494800-74497000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:74494800-74498000	Enhancers	Primary T cells from cord blood	blood
35	chr15:74495000-74497400	Weak transcription	Right Atrium	heart
36	chr15:74495200-74496400	Weak transcription	Fetal Brain Female	brain
37	chr15:74495200-74496800	Weak transcription	Lung	lung
38	chr15:74495200-74497000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr15:74495400-74496600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:74495400-74496800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr15:74495400-74497000	Enhancers	Placenta	Placenta
42	chr15:74495400-74497400	Weak transcription	Right Ventricle	heart
43	chr15:74495400-74497600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:74495400-74497600	Weak transcription	Thymus	Thymus
45	chr15:74495600-74496600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:74495600-74496600	Enhancers	Fetal Kidney	kidney
47	chr15:74495600-74496800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr15:74495600-74496800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr15:74495600-74496800	Flanking Active TSS	A549	lung
50	chr15:74495600-74497000	Enhancers	Fetal Stomach	stomach

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