Variant report

Variant	rs1871498
Chromosome Location	chr15:59954853-59954854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59953943..59955964-chr15:59959254..59962157,2	K562	blood:
2	chr15:59953614..59955530-chr15:59965448..59967216,2	K562	blood:
3	chr15:59953267..59956180-chr15:59978902..59983240,4	K562	blood:
4	chr15:59949015..59951942-chr15:59953463..59956505,3	MCF-7	breast:
5	chr15:59953943..59956937-chr15:59959254..59962353,4	K562	blood:
6	chr15:59952501..59955288-chr15:59979374..59982018,3	K562	blood:

Variant related genes	Relation type
ENSG00000259238	Chromatin interaction
ENSG00000140307	Chromatin interaction
ENSG00000140299	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10851661	0.92[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10851662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10851663	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11071463	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11071464	0.92[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12101518	1.00[AMR][1000 genomes]
rs12101627	1.00[AMR][1000 genomes]
rs16941555	1.00[AMR][1000 genomes]
rs16941810	1.00[AMR][1000 genomes]
rs2307274	0.84[ASW][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4775196	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6151431	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6151435	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6151476	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6151537	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6151550	1.00[AMR][1000 genomes]
rs6151587	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6494134	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7162788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7180507	1.00[AMR][1000 genomes]
rs7180620	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74019651	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8039996	0.92[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8041511	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9806322	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1043693	chr15:59944471-59971500	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59949400-59960200	Weak transcription	Fetal Heart	heart
2	chr15:59949800-59957200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:59949800-59957200	Weak transcription	Spleen	Spleen
4	chr15:59949800-59963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:59949800-59964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:59949800-59968000	Weak transcription	Stomach Mucosa	stomach
7	chr15:59949800-59968400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:59949800-59980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:59950000-59963200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:59950200-59955200	Weak transcription	Fetal Brain Female	brain
11	chr15:59950200-59955400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:59950200-59955600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:59950200-59955800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:59950200-59956800	Weak transcription	Fetal Intestine Small	intestine
15	chr15:59950200-59956800	Weak transcription	Fetal Stomach	stomach
16	chr15:59950200-59956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:59950200-59957000	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:59950200-59958400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:59950200-59959200	Weak transcription	Fetal Brain Male	brain
20	chr15:59950200-59960200	Weak transcription	Colonic Mucosa	Colon
21	chr15:59950200-59961200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:59950200-59963400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:59950200-59963400	Weak transcription	Brain Angular Gyrus	brain
24	chr15:59950200-59963400	Weak transcription	Ovary	ovary
25	chr15:59950200-59964000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:59950200-59964000	Weak transcription	Gastric	stomach
27	chr15:59950200-59964000	Weak transcription	Lung	lung
28	chr15:59950200-59964000	Weak transcription	Small Intestine	intestine
29	chr15:59950200-59967800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:59950200-59968400	Weak transcription	Right Ventricle	heart
31	chr15:59950200-59968800	Weak transcription	Aorta	Aorta
32	chr15:59950400-59956800	Weak transcription	Thymus	Thymus
33	chr15:59950400-59958400	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:59950400-59960200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:59950400-59964000	Weak transcription	Pancreas	Pancrea
36	chr15:59950400-59964000	Weak transcription	Psoas Muscle	Psoas
37	chr15:59950400-59965600	Weak transcription	Brain Substantia Nigra	brain
38	chr15:59950400-59968800	Weak transcription	Esophagus	oesophagus
39	chr15:59950400-59979600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:59950600-59955200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:59950600-59957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:59950800-59956600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:59950800-59961600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:59951000-59978400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:59951200-59958600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:59951400-59956400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:59951400-59960600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:59951400-59964600	Strong transcription	HUVEC	blood vessel
49	chr15:59951400-59965400	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr15:59951400-59972600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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