Variant report

Variant	rs3780418
Chromosome Location	chr9:100677100-100677101
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86397392..86400390-chr9:100675486..100677661,2	K562	blood:
2	chr9:100662549..100664772-chr9:100675385..100677486,2	K562	blood:
3	chr9:100674231..100678302-chr9:100744904..100747134,4	MCF-7	breast:
4	chr9:100677016..100678517-chr9:100817759..100820189,2	MCF-7	breast:
5	chr9:100675954..100709047-chr9:100737887..100755543,175	K562	blood:

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction
ENSG00000236896	Chromatin interaction
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10984193	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10984297	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10984349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10984375	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10984405	0.83[ASN][1000 genomes]
rs10984462	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10984478	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10984484	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10984499	0.81[ASN][1000 genomes]
rs10984588	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10984599	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1127703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12235434	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237296	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377604	0.84[ASN][1000 genomes]
rs1475695	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1475696	0.82[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs17346310	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17431614	0.97[ASN][1000 genomes]
rs17431934	0.84[ASN][1000 genomes]
rs3780416	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780417	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3824496	0.97[ASN][1000 genomes]
rs4498663	0.85[EUR][1000 genomes]
rs4618817	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743145	0.97[ASN][1000 genomes]
rs62574034	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62574035	0.83[EUR][1000 genomes]
rs66990486	0.97[ASN][1000 genomes]
rs67500034	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67975003	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68053069	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs68112593	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7024281	0.89[AMR][1000 genomes]
rs7025609	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7030887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7030907	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7040232	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72753548	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72753572	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72753587	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs755109	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7855917	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7861658	0.97[ASN][1000 genomes]
rs7864655	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv3483721	chr9:100675531-100678988	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv3483722	chr9:100675531-100678988	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	7 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	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:100665400-100679000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:100665600-100678200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:100667200-100679400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:100667200-100684200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:100669600-100678600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
8	chr9:100669600-100678800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr9:100669800-100678400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:100670000-100678600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr9:100670000-100684200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:100670200-100678600	Strong transcription	Liver	Liver
13	chr9:100670200-100678600	Strong transcription	Placenta	Placenta
14	chr9:100670200-100678600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr9:100670400-100678400	Strong transcription	Dnd41	blood
16	chr9:100670400-100679400	Strong transcription	Thymus	Thymus
17	chr9:100670800-100684200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:100671000-100677400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:100671000-100677800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:100671000-100678400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:100671200-100680200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr9:100671400-100678800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:100671600-100678200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:100671600-100678600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:100671600-100678600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr9:100671600-100678600	Strong transcription	Fetal Thymus	thymus
27	chr9:100671600-100678800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:100671800-100678400	Strong transcription	Primary B cells from cord blood	blood
29	chr9:100671800-100678600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:100671800-100680200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr9:100672000-100679800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr9:100672000-100679800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr9:100672200-100678200	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr9:100672200-100678600	Strong transcription	HSMM	muscle
35	chr9:100672800-100677800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr9:100672800-100684200	Weak transcription	Esophagus	oesophagus
37	chr9:100673000-100684000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:100673200-100682200	Weak transcription	Stomach Mucosa	stomach
39	chr9:100673400-100681000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:100673600-100684000	Weak transcription	NHDF-Ad	bronchial
41	chr9:100673800-100678600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr9:100673800-100680000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:100673800-100683400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:100673800-100683400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:100673800-100684000	Weak transcription	Aorta	Aorta
46	chr9:100673800-100684200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:100673800-100684400	Weak transcription	Spleen	Spleen
48	chr9:100674200-100678800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr9:100674400-100678000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:100674600-100682800	Weak transcription	Brain Cingulate Gyrus	brain

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