Variant report

Variant	rs11489600
Chromosome Location	chr7:102948040-102948041
allele	C/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	POLR2A	chr7:102947692-102948716	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr7:102947995-102948251	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:102947784-102948720	K562	blood:	n/a	n/a
4	POLR2A	chr7:102947731-102948158	HepG2	liver:	n/a	n/a
5	NFIC	chr7:102947903-102948860	SK-N-SH	brain:	n/a	chr7:102948448-102948465 chr7:102948449-102948466 chr7:102948697-102948713 chr7:102948448-102948464
6	POLR2A	chr7:102947788-102949927	MCF-7	breast:	n/a	n/a
7	POLR2A	chr7:102947937-102949517	Hela-S3	cervix:	n/a	n/a
8	EBF1	chr7:102947973-102948232	GM12878	blood:	n/a	n/a
9	FOXA1	chr7:102948019-102948266	T-47D	breast:	n/a	chr7:102948216-102948228
10	POLR2A	chr7:102947279-102948102	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr7:102947891-102948124	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:102946980..102949686-chr7:103019517..103021353,2	K562	blood:
2	chr7:102946587..102948728-chr7:103004817..103007123,2	MCF-7	breast:
3	chr7:102945649..102948219-chr7:102988221..102989822,2	MCF-7	breast:
4	chr7:102946730..102948829-chr7:102955454..102957665,3	K562	blood:
5	chr7:102937906..102941982-chr7:102947783..102950919,3	MCF-7	breast:
6	chr7:102945838..102949503-chr7:103019550..103022202,3	K562	blood:

Variant related genes	Relation type
PMPCB	TF binding region
ENSG00000235354	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12667428	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12705114	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12705115	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13221892	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13228258	0.83[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[ASN][1000 genomes]
rs13232414	0.82[ASN][1000 genomes]
rs2074624	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3959214	0.88[ASN][1000 genomes]
rs4729905	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4729907	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs4729909	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv831084	chr7:102778908-102964970	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102938400-102957000	Weak transcription	Spleen	Spleen
2	chr7:102938600-102951400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:102938600-102957000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:102938600-102984200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:102938800-102957000	Weak transcription	Aorta	Aorta
6	chr7:102939000-102965200	Weak transcription	Right Ventricle	heart
7	chr7:102939000-102969200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr7:102939200-102949600	Strong transcription	Left Ventricle	heart
9	chr7:102939200-102962000	Weak transcription	Right Atrium	heart
10	chr7:102939200-102967400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr7:102939200-102968400	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr7:102939200-102968400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:102939200-102972400	Strong transcription	Fetal Thymus	thymus
14	chr7:102939400-102948400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr7:102939400-102950800	Weak transcription	Small Intestine	intestine
16	chr7:102939400-102958800	Weak transcription	Gastric	stomach
17	chr7:102939400-102964800	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr7:102939400-102965600	Strong transcription	Fetal Lung	lung
19	chr7:102939400-102966800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr7:102939400-102967800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr7:102939400-102967800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:102939400-102968000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr7:102939400-102968000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr7:102939400-102968200	Strong transcription	Placenta	Placenta
25	chr7:102939400-102968200	Strong transcription	HSMM	muscle
26	chr7:102939400-102969800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr7:102939600-102948200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr7:102939600-102948800	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr7:102939600-102949600	Strong transcription	Thymus	Thymus
30	chr7:102939600-102963200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr7:102939600-102965400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr7:102939600-102966800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr7:102939600-102968000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:102939600-102968000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:102939600-102968000	Strong transcription	Fetal Intestine Large	intestine
36	chr7:102939600-102968000	Strong transcription	Fetal Muscle Leg	muscle
37	chr7:102939600-102968400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:102939600-102968400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:102939600-102968600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:102939600-102969800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:102939600-102970000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:102939800-102949600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:102939800-102952600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:102939800-102959600	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr7:102939800-102960600	Strong transcription	NH-A	brain
46	chr7:102939800-102960800	Strong transcription	Brain Germinal Matrix	brain
47	chr7:102939800-102962400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:102939800-102968000	Strong transcription	Adipose Nuclei	Adipose
49	chr7:102939800-102968000	Strong transcription	Osteobl	bone
50	chr7:102939800-102968200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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