Variant report

Variant	rs474351
Chromosome Location	chr15:41388971-41388972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41384971..41389195-chr15:41407627..41410447,4	MCF-7	breast:
2	chr15:41388020..41390130-chr15:41405775..41409320,4	K562	blood:

Variant related genes	Relation type
ENSG00000128908	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10152296	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11070319	1.00[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs11070320	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11630905	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs16971263	0.88[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs16971264	1.00[MEX][hapmap]
rs16971413	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs16971463	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16971507	1.00[MEX][hapmap]
rs2007255	1.00[MEX][hapmap];0.89[YRI][hapmap]
rs2412573	0.86[YRI][hapmap]
rs2412599	0.82[LWK][hapmap];1.00[TSI][hapmap]
rs2412600	0.84[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs28455970	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2899010	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2925344	1.00[MEX][hapmap]
rs2925348	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2925349	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2927067	0.84[AFR][1000 genomes]
rs2928147	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2928149	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2928150	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2928154	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2947492	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2947495	0.90[AFR][1000 genomes]
rs2947496	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2955812	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs3101435	0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs3101438	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs3101440	1.00[MEX][hapmap]
rs3101441	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4468583	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs480549	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs487779	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4923894	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4923895	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4924533	1.00[ASW][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4924534	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs496499	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs513680	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs518137	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs525551	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs538903	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs56955512	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs57008457	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs57385441	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs58142514	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs59405359	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs690773	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs691069	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs691445	1.00[EUR][1000 genomes]
rs691722	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs692703	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7162003	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7165020	1.00[GIH][hapmap]
rs7167166	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7169092	1.00[MEX][hapmap]
rs7172555	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7173146	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7174513	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs7178308	1.00[GIH][hapmap]
rs7183191	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs73399092	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8030958	1.00[MEX][hapmap]
rs8032956	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8034461	0.94[AMR][1000 genomes]
rs8035532	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8043232	0.88[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs9806344	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9806730	1.00[MEX][hapmap]

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	nsv1053462	chr15:41270067-41396094	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41334600-41389000	Strong transcription	Primary T helper cells PMA-I stimulated	--
2	chr15:41341600-41389000	Strong transcription	Liver	Liver
3	chr15:41354200-41389200	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr15:41354600-41389000	Strong transcription	Duodenum Mucosa	Duodenum
5	chr15:41354800-41389200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:41355000-41389400	Strong transcription	Placenta	Placenta
7	chr15:41355000-41392000	Strong transcription	Fetal Thymus	thymus
8	chr15:41355000-41392400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:41355000-41393800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:41355400-41389200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:41355400-41390200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:41355400-41393200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:41355600-41390800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr15:41355800-41389200	Strong transcription	Dnd41	blood
15	chr15:41355800-41391000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:41356600-41389000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr15:41356800-41391000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:41356800-41392200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:41358000-41393600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:41358200-41392000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:41360400-41389200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:41361200-41407200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:41365200-41391000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:41365400-41389800	Strong transcription	Stomach Smooth Muscle	stomach
25	chr15:41369000-41391800	Weak transcription	Right Atrium	heart
26	chr15:41369600-41389000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr15:41370800-41390800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr15:41371800-41390800	Weak transcription	Stomach Mucosa	stomach
29	chr15:41372800-41392400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:41373200-41389800	Strong transcription	Primary B cells from cord blood	blood
31	chr15:41375800-41389800	Strong transcription	HSMM	muscle
32	chr15:41378000-41397600	Weak transcription	Small Intestine	intestine
33	chr15:41379200-41389200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr15:41380400-41393400	Strong transcription	Fetal Intestine Small	intestine
35	chr15:41381400-41389000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:41381400-41389200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:41382000-41389000	Strong transcription	HMEC	breast
38	chr15:41382600-41389200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:41383200-41406800	Weak transcription	A549	lung
40	chr15:41383800-41407400	Weak transcription	Esophagus	oesophagus
41	chr15:41384000-41407400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:41384200-41389000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:41384200-41391400	Strong transcription	Hela-S3	cervix
44	chr15:41384200-41395600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:41384400-41396000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:41384400-41396000	Weak transcription	Psoas Muscle	Psoas
47	chr15:41384400-41407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:41385200-41406000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr15:41386200-41398400	Weak transcription	Gastric	stomach
50	chr15:41386200-41407400	Weak transcription	Aorta	Aorta

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