Variant report

Variant	rs173224
Chromosome Location	chr15:33191023-33191024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12591087	0.91[JPT][hapmap]
rs12595789	0.86[JPT][hapmap]
rs1562932	0.82[JPT][hapmap]
rs17228887	0.91[JPT][hapmap]
rs347931	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs534755	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8027615	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv832962	chr15:33111517-33239736	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS 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	4 gene(s)	inside rSNPs	diseases
9	nsv903980	chr15:33149087-33264201	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv568917	chr15:33167171-33304172	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription 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	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs173224	SCG5	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33147000-33191400	Weak transcription	Lung	lung
2	chr15:33149000-33202000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr15:33154400-33192800	Weak transcription	Colonic Mucosa	Colon
4	chr15:33154400-33216800	Weak transcription	Fetal Thymus	thymus
5	chr15:33155000-33208200	Weak transcription	Fetal Kidney	kidney
6	chr15:33160000-33201800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:33162200-33202400	Weak transcription	Gastric	stomach
8	chr15:33166000-33202400	Weak transcription	Pancreas	Pancrea
9	chr15:33166200-33211800	Weak transcription	HSMMtube	muscle
10	chr15:33170800-33196200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:33170800-33200400	Weak transcription	NH-A	brain
12	chr15:33178800-33197600	Weak transcription	Osteobl	bone
13	chr15:33179000-33198000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:33180600-33196600	Weak transcription	Placenta	Placenta
15	chr15:33181800-33198800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:33181800-33201000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:33182000-33200600	Weak transcription	Fetal Stomach	stomach
18	chr15:33183600-33195000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:33185800-33191400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:33188800-33192200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:33188800-33193000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr15:33189600-33191200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:33189600-33192400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:33189800-33192400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:33189800-33192800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr15:33190000-33192400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:33190000-33192400	Strong transcription	HSMM	muscle
28	chr15:33190000-33192600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:33190200-33191600	Enhancers	H1 Cell Line	embryonic stem cell
30	chr15:33190200-33192400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:33190200-33192400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:33190200-33192400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:33190400-33192400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr15:33190400-33192400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:33190600-33191400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:33190600-33191800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:33190600-33192400	Strong transcription	Thymus	Thymus
38	chr15:33190800-33191200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr15:33190800-33191400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr15:33190800-33191400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:33190800-33191400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr15:33190800-33191600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr15:33190800-33191600	Strong transcription	NHLF	lung
44	chr15:33190800-33192000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:33190800-33192400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:33190800-33192600	Enhancers	Primary B cells from peripheral blood	blood
47	chr15:33190800-33192600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr15:33190800-33192800	Enhancers	Primary B cells from cord blood	blood
49	chr15:33190800-33193000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:33191000-33191400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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