Variant report

Variant	rs3764474
Chromosome Location	chr18:29206121-29206122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29206102..29208678-chr18:29263634..29265873,3	MCF-7	breast:
2	chr18:29145542..29146264-chr18:29205706..29207014,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259985	Chromatin interaction
ENSG00000118276	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1026122	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1026123	0.87[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1078998	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12962843	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1612691	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1621308	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1667262	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1667274	0.85[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1667275	0.86[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1667276	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1667279	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1667280	0.89[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1667281	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1667283	0.84[ASN][1000 genomes]
rs1667284	0.89[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1667286	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1791161	0.89[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1791169	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1791171	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1791181	0.82[ASN][1000 genomes]
rs1791192	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1791193	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1791221	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2595360	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794878	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794882	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41447647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4799311	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6506935	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7232056	0.88[EUR][1000 genomes]
rs7242641	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8097755	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895888	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs974676	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs974677	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9950458	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1816420	chr18:29201648-29207155	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29191400-29207000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr18:29191400-29207800	Weak transcription	Fetal Intestine Large	intestine
3	chr18:29191800-29207800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:29192200-29206200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr18:29192400-29217400	Weak transcription	Left Ventricle	heart
6	chr18:29194800-29226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr18:29197200-29210600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr18:29197400-29207800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr18:29197600-29206400	Weak transcription	Fetal Intestine Small	intestine
10	chr18:29197600-29224800	Weak transcription	Brain Anterior Caudate	brain
11	chr18:29197600-29224800	Weak transcription	Brain Germinal Matrix	brain
12	chr18:29197800-29206200	Weak transcription	GM12878-XiMat	blood
13	chr18:29199200-29212400	Weak transcription	Aorta	Aorta
14	chr18:29199800-29217200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr18:29200000-29222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr18:29200200-29208600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr18:29200200-29222000	Weak transcription	HMEC	breast
18	chr18:29200400-29210400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:29200800-29206600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr18:29201600-29206200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr18:29202800-29235000	Weak transcription	Pancreas	Pancrea
22	chr18:29202800-29240200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr18:29203000-29208000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr18:29203200-29217000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr18:29203400-29211000	Weak transcription	HUVEC	blood vessel
26	chr18:29203800-29207800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr18:29203800-29220200	Weak transcription	Ovary	ovary
28	chr18:29203800-29226000	Weak transcription	Fetal Lung	lung
29	chr18:29203800-29227400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr18:29204000-29210000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr18:29204000-29210400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr18:29204000-29210400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr18:29204000-29213600	Weak transcription	Thymus	Thymus
34	chr18:29204000-29228400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr18:29204200-29223200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr18:29204400-29220800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr18:29204400-29228400	Weak transcription	Psoas Muscle	Psoas
38	chr18:29204600-29213600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr18:29204600-29238600	Weak transcription	Gastric	stomach
40	chr18:29204800-29206200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:29204800-29206200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr18:29204800-29206400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr18:29204800-29206400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr18:29204800-29208200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr18:29204800-29209000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:29204800-29209000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr18:29205000-29215600	Weak transcription	Fetal Stomach	stomach
48	chr18:29205000-29215800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr18:29205000-29227400	Weak transcription	A549	lung
50	chr18:29205400-29207000	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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