Variant report

Variant	rs563542
Chromosome Location	chr7:16654291-16654292
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16647541..16650601-chr7:16652797..16655866,3	K562	blood:
2	chr7:16653579..16656411-chr7:16684734..16687056,2	MCF-7	breast:
3	chr7:16652156..16654551-chr7:16658497..16660099,2	K562	blood:

Variant related genes	Relation type
ENSG00000136261	Chromatin interaction
ENSG00000106524	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs4719472	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4721517	0.84[ASN][1000 genomes]
rs476489	0.84[ASN][1000 genomes]
rs481026	0.90[ASN][1000 genomes]
rs503157	0.84[ASN][1000 genomes]
rs511938	0.90[ASN][1000 genomes]
rs514114	0.84[ASN][1000 genomes]
rs516038	0.84[ASN][1000 genomes]
rs541797	0.84[ASN][1000 genomes]
rs561370	0.84[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	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1028125	chr7:16529160-16847225	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv830912	chr7:16623196-16791974	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv887758	chr7:16632561-16668034	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1024059	chr7:16639432-16836425	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv522819	chr7:16639615-16655387	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv887759	chr7:16642995-16686940	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16635600-16654800	Weak transcription	Spleen	Spleen
2	chr7:16636400-16682600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:16637400-16668400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:16637800-16654800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:16637800-16661600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:16637800-16664800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:16638000-16656200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr7:16638000-16658800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:16638000-16660200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr7:16638000-16670800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:16638200-16655200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:16638200-16656200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:16638200-16659800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:16638400-16654800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr7:16638400-16661600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:16638400-16670000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:16638400-16670200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:16639000-16655000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:16639000-16656600	Strong transcription	Left Ventricle	heart
20	chr7:16639600-16655000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:16640400-16668000	Weak transcription	HSMMtube	muscle
22	chr7:16640600-16663400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr7:16640800-16659800	Weak transcription	NHEK	skin
24	chr7:16640800-16677000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:16642000-16674000	Weak transcription	Psoas Muscle	Psoas
26	chr7:16643000-16659800	Weak transcription	Fetal Heart	heart
27	chr7:16643400-16654800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:16643400-16656200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr7:16643600-16663000	Weak transcription	HUVEC	blood vessel
30	chr7:16643600-16676000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr7:16643600-16681000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr7:16643800-16654600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr7:16643800-16654800	Weak transcription	Brain Germinal Matrix	brain
34	chr7:16643800-16670200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:16644400-16677600	Weak transcription	Brain Substantia Nigra	brain
36	chr7:16644600-16654800	Weak transcription	Aorta	Aorta
37	chr7:16644600-16654800	Weak transcription	NHLF	lung
38	chr7:16644600-16656400	Weak transcription	Colon Smooth Muscle	Colon
39	chr7:16644600-16678000	Weak transcription	Fetal Brain Male	brain
40	chr7:16646000-16656400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:16646200-16656400	Weak transcription	Esophagus	oesophagus
42	chr7:16646600-16683000	Weak transcription	Colonic Mucosa	Colon
43	chr7:16646800-16656200	Weak transcription	Lung	lung
44	chr7:16646800-16656200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:16647600-16666400	Strong transcription	Liver	Liver
46	chr7:16647800-16654800	Weak transcription	Right Ventricle	heart
47	chr7:16648200-16654800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:16648200-16654800	Weak transcription	Thymus	Thymus
49	chr7:16648200-16668200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:16648400-16656000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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