Variant report

Variant	rs9901109
Chromosome Location	chr17:38379848-38379849
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38374106..38377261-chr17:38378307..38382923,6	K562	blood:
2	chr17:38373137..38377221-chr17:38377340..38382604,9	K562	blood:

Variant related genes	Relation type
ENSG00000171475	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11078940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs13706	1.00[CEU][hapmap]
rs16965666	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs16965687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2280400	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2314338	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs28537537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28663197	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3744806	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs4077125	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4566234	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs56029626	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6503539	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7211770	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs72836635	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72836636	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72836639	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72836641	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72836642	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72836648	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7359537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7405635	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8066144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8073925	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8080931	0.81[ASN][1000 genomes]
rs8082192	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs9303286	1.00[CEU][hapmap]
rs9891718	0.82[ASN][1000 genomes]
rs9892404	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9892946	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9893520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9895163	0.82[ASN][1000 genomes]
rs9897092	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9904021	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9904270	1.00[CEU][hapmap]
rs9906409	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9907683	0.84[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs9908034	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9908257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9911840	0.80[ASN][1000 genomes]
rs9912082	0.81[ASN][1000 genomes]
rs9916460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9916782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3507998	chr17:38377409-38380022	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv3507999	chr17:38377409-38380022	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38376600-38380000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:38376600-38380200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:38376600-38380800	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:38376600-38380800	Weak transcription	Fetal Lung	lung
5	chr17:38376600-38389200	Weak transcription	Esophagus	oesophagus
6	chr17:38376600-38389800	Weak transcription	Colonic Mucosa	Colon
7	chr17:38376600-38389800	Weak transcription	Ovary	ovary
8	chr17:38376600-38390400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:38376600-38392200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:38376600-38393200	Weak transcription	Fetal Heart	heart
11	chr17:38376600-38400400	Weak transcription	Psoas Muscle	Psoas
12	chr17:38376600-38412400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr17:38376600-38416800	Weak transcription	Aorta	Aorta
14	chr17:38376800-38380200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:38376800-38380200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:38376800-38380200	Weak transcription	K562	blood
17	chr17:38376800-38380200	Weak transcription	NH-A	brain
18	chr17:38376800-38380200	Weak transcription	Osteobl	bone
19	chr17:38376800-38380400	Weak transcription	NHLF	lung
20	chr17:38376800-38380600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr17:38376800-38380800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:38376800-38380800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr17:38376800-38380800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:38376800-38380800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr17:38376800-38380800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:38376800-38380800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:38376800-38380800	Weak transcription	Right Ventricle	heart
28	chr17:38376800-38380800	Weak transcription	HSMM	muscle
29	chr17:38376800-38380800	Weak transcription	NHDF-Ad	bronchial
30	chr17:38376800-38381000	Weak transcription	Right Atrium	heart
31	chr17:38376800-38381200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr17:38376800-38381800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr17:38376800-38382800	Weak transcription	Fetal Intestine Large	intestine
34	chr17:38376800-38383000	Weak transcription	Fetal Intestine Small	intestine
35	chr17:38376800-38383000	Weak transcription	Thymus	Thymus
36	chr17:38376800-38383800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr17:38376800-38386800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr17:38376800-38387200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr17:38376800-38388600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:38376800-38389200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr17:38376800-38389200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr17:38376800-38389200	Weak transcription	HUVEC	blood vessel
43	chr17:38376800-38389600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr17:38376800-38389600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:38376800-38390600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr17:38376800-38391400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr17:38376800-38391600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr17:38376800-38393600	Weak transcription	HMEC	breast
49	chr17:38377000-38380200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr17:38377000-38383400	Weak transcription	Fetal Thymus	thymus

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