Variant report

Variant	rs6598237
Chromosome Location	chr15:99877293-99877294
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	chr15:99875104..99877834-chr15:99882696..99885261,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1033035	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1033036	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10794475	0.86[YRI][hapmap]
rs10902543	0.90[JPT][hapmap];0.96[YRI][hapmap]
rs10902544	0.88[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11247074	0.84[AFR][1000 genomes]
rs11247075	0.84[AFR][1000 genomes]
rs11247079	0.94[ASW][hapmap];0.88[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11247080	0.81[JPT][hapmap]
rs11247081	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11853278	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11853850	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs12592075	0.83[ASW][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12906357	0.89[YRI][hapmap]
rs12912927	0.82[CEU][hapmap]
rs12913897	0.83[ASW][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1472989	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812344	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1876927	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2048305	0.82[CEU][hapmap]
rs2089707	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs2175225	0.96[ASN][1000 genomes]
rs28520505	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28696045	0.84[AFR][1000 genomes]
rs3851679	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3863401	0.82[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4965225	0.86[YRI][hapmap]
rs4965474	0.91[JPT][hapmap]
rs58946939	0.92[ASN][1000 genomes]
rs6598238	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7162949	0.86[YRI][hapmap]
rs7167119	0.96[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7167542	0.98[ASN][1000 genomes]
rs7167899	0.82[CEU][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7168227	0.94[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7169906	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7171970	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173844	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7181739	0.87[AFR][1000 genomes]
rs7182425	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182675	0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7498053	0.82[CEU][hapmap]
rs8036160	0.88[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8040850	0.92[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8041923	0.96[CEU][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8042249	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8042667	0.94[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS 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	30 gene(s)	inside rSNPs	diseases
9	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
10	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
14	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
16	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
17	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
19	nsv1052683	chr15:99869631-99924685	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
20	nsv542521	chr15:99869631-99924685	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6598237	COL8A2	trans	parietal	SCAN
rs6598237	LRRK1	cis	parietal	SCAN
rs6598237	TTC23	cis	lymphoblastoid	seeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99859400-99906600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:99863200-99881200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:99863200-99899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:99864400-99902200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:99864800-99881400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:99864800-99884200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr15:99865200-99880600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:99866800-99877400	Weak transcription	Right Ventricle	heart
9	chr15:99866800-99877800	Weak transcription	Psoas Muscle	Psoas
10	chr15:99866800-99881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:99866800-99882400	Weak transcription	Gastric	stomach
12	chr15:99867000-99880600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:99867200-99877400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:99867200-99926600	Weak transcription	NHEK	skin
15	chr15:99869200-99880200	Weak transcription	HepG2	liver
16	chr15:99869200-99882000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:99869600-99893400	Weak transcription	Aorta	Aorta
18	chr15:99869800-99884600	Weak transcription	GM12878-XiMat	blood
19	chr15:99870200-99884400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:99870200-99884600	Weak transcription	Primary B cells from cord blood	blood
21	chr15:99871200-99893000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr15:99871400-99888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:99871600-99880400	Weak transcription	A549	lung
24	chr15:99871600-99895200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:99872000-99879200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:99872000-99893200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:99872000-99906600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:99872000-99912600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:99872400-99880200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:99872600-99909000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:99872800-99906200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:99872800-99911400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:99873200-99877400	Weak transcription	Fetal Intestine Small	intestine
34	chr15:99873200-99884000	Weak transcription	Right Atrium	heart
35	chr15:99873200-99894800	Weak transcription	Brain Angular Gyrus	brain
36	chr15:99873400-99886200	Weak transcription	Esophagus	oesophagus
37	chr15:99874200-99880400	Weak transcription	NHLF	lung
38	chr15:99874200-99893200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr15:99874400-99881400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:99874400-99887600	Weak transcription	Spleen	Spleen
41	chr15:99874400-99893200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:99874400-99893400	Weak transcription	Lung	lung
43	chr15:99874400-99903400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:99874600-99879000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:99874600-99895400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:99874600-99906600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr15:99874800-99877400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:99875000-99880200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:99875400-99878200	Strong transcription	Fetal Thymus	thymus
50	chr15:99875800-99877400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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