Variant report

Variant	rs7178948
Chromosome Location	chr15:100119117-100119118
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:100118981..100120902-chr15:100121379..100123708,2	K562	blood:
2	chr15:100111468..100113538-chr15:100118782..100121067,2	K562	blood:
3	chr15:100117617..100121955-chr15:100124250..100127287,4	K562	blood:
4	chr15:100104593..100107868-chr15:100116862..100120371,3	MCF-7	breast:
5	chr15:100104524..100107362-chr15:100116776..100120045,3	K562	blood:
6	chr15:100115012..100117156-chr15:100118010..100120795,3	K562	blood:
7	chr15:100104501..100107809-chr15:100115023..100120285,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11247113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11247118	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs11247120	0.88[CEU][hapmap];0.85[CHB][hapmap];0.85[YRI][hapmap]
rs12441844	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593181	0.83[ASN][1000 genomes]
rs12898848	0.80[CHB][hapmap]
rs12913830	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.83[ASN][1000 genomes]
rs188977	0.80[YRI][hapmap]
rs2033547	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs2164058	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2570808	0.81[ASW][hapmap]
rs28716652	0.90[EUR][1000 genomes]
rs3743180	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4273018	0.81[CHB][hapmap]
rs4965533	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.83[ASN][1000 genomes]
rs4965534	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs4965536	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.99[MKK][hapmap];0.80[YRI][hapmap];0.84[ASN][1000 genomes]
rs59812744	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62042267	0.84[ASN][1000 genomes]
rs7163683	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172418	0.83[GIH][hapmap]
rs7176008	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7179518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7181767	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8024784	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036535	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8037206	0.89[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv904558	chr15:100019382-100171684	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7178948	LYSMD4	cis	parietal	SCAN
rs7178948	LYSMD4	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100107400-100120200	Weak transcription	Lung	lung
2	chr15:100107400-100134200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:100107400-100134200	Weak transcription	Pancreas	Pancrea
4	chr15:100107800-100124800	Weak transcription	Fetal Stomach	stomach
5	chr15:100108000-100142000	Weak transcription	Thymus	Thymus
6	chr15:100108200-100120200	Weak transcription	Fetal Thymus	thymus
7	chr15:100108200-100125200	Weak transcription	Fetal Muscle Leg	muscle
8	chr15:100108400-100124600	Weak transcription	Brain Germinal Matrix	brain
9	chr15:100109000-100124000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:100109000-100140200	Weak transcription	Hela-S3	cervix
11	chr15:100109600-100119200	Weak transcription	NH-A	brain
12	chr15:100109600-100120200	Weak transcription	Right Atrium	heart
13	chr15:100109600-100120400	Weak transcription	HUVEC	blood vessel
14	chr15:100109600-100124000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:100109600-100125800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr15:100109600-100126200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:100109600-100132200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr15:100109800-100122000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:100113800-100120400	Weak transcription	Gastric	stomach
20	chr15:100113800-100120400	Weak transcription	Small Intestine	intestine
21	chr15:100114200-100124000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:100114400-100119200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:100114400-100124400	Weak transcription	A549	lung
24	chr15:100114600-100120200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr15:100114800-100119200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr15:100115000-100120000	Weak transcription	Right Ventricle	heart
27	chr15:100115000-100122800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:100115000-100138800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:100115200-100120000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:100115400-100120200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:100115800-100120000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:100115800-100120000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:100115800-100120400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:100115800-100121200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:100116400-100124000	Weak transcription	Primary B cells from cord blood	blood
36	chr15:100117000-100123000	Enhancers	Liver	Liver
37	chr15:100117400-100119800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr15:100117600-100119200	Enhancers	Colon Smooth Muscle	Colon
39	chr15:100117600-100119400	Enhancers	Brain Angular Gyrus	brain
40	chr15:100117600-100119600	Enhancers	Brain Hippocampus Middle	brain
41	chr15:100117600-100120800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:100117600-100120800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr15:100117600-100121000	Enhancers	Adipose Nuclei	Adipose
44	chr15:100117600-100123600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr15:100117800-100119600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:100117800-100120000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:100118200-100119400	Enhancers	Brain Substantia Nigra	brain
48	chr15:100118200-100120600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:100118200-100121000	Enhancers	Primary B cells from peripheral blood	blood
50	chr15:100118400-100119200	Enhancers	Aorta	Aorta

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