Variant report

Variant	rs1728232
Chromosome Location	chr1:113564644-113564645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113495044..113497639-chr1:113562401..113565157,2	K562	blood:
2	chr1:113564257..113567522-chr1:113568390..113572555,4	K562	blood:
3	chr1:113564641..113566837-chr1:113568390..113571162,2	K562	blood:
4	chr1:113496138..113497721-chr1:113563292..113564960,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1049434	0.88[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs10857980	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs11102573	0.94[ASN][1000 genomes]
rs11102574	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11102575	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11102576	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11102577	0.81[ASN][1000 genomes]
rs11102582	0.87[JPT][hapmap]
rs11584099	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11584535	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11588345	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11590170	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11590174	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12066274	0.82[ASN][1000 genomes]
rs12128904	0.92[ASN][1000 genomes]
rs12129863	0.94[ASN][1000 genomes]
rs1216603	0.95[EUR][1000 genomes]
rs1216772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1216773	0.94[ASN][1000 genomes]
rs1216775	0.94[ASN][1000 genomes]
rs1216779	0.94[ASN][1000 genomes]
rs1216781	0.94[JPT][hapmap]
rs1216783	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1216784	0.90[ASN][1000 genomes]
rs1216785	0.93[ASN][1000 genomes]
rs1216790	0.81[ASN][1000 genomes]
rs12184285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12354228	0.93[ASN][1000 genomes]
rs12744009	0.89[JPT][hapmap]
rs12745675	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12746771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12754835	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1539624	0.84[CEU][hapmap]
rs1544227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1627925	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1629027	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs17014850	0.94[ASN][1000 genomes]
rs17030901	0.94[ASN][1000 genomes]
rs17030905	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17030974	0.94[JPT][hapmap]
rs1728218	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1728219	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1728238	0.89[JPT][hapmap]
rs1766862	0.94[JPT][hapmap]
rs1778024	0.94[JPT][hapmap]
rs1778025	0.94[JPT][hapmap]
rs1983929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2769259	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2798691	0.94[ASN][1000 genomes]
rs2798692	0.94[ASN][1000 genomes]
rs34233065	0.94[ASN][1000 genomes]
rs34565381	0.86[ASN][1000 genomes]
rs3789592	0.88[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs3889656	0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3951437	0.81[ASN][1000 genomes]
rs61818171	0.94[ASN][1000 genomes]
rs61818172	0.94[ASN][1000 genomes]
rs61818173	0.94[ASN][1000 genomes]
rs61818174	0.94[ASN][1000 genomes]
rs61818176	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6537764	0.82[EUR][1000 genomes]
rs6537765	0.92[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs6656041	0.94[ASN][1000 genomes]
rs6656311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6663872	0.82[EUR][1000 genomes]
rs6681037	0.81[CEU][hapmap]
rs71659385	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169	0.88[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs7556664	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs773430	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs773432	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs773433	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs773434	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs773435	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773436	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs773439	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs773440	0.87[ASN][1000 genomes]
rs773442	0.96[EUR][1000 genomes]
rs9633370	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs9787311	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active 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 miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
10	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1728232	OLFML3	cis	cerebellum	SCAN
rs1728232	SLC6A17	cis	parietal	SCAN
rs1728232	LRIG2	cis	cerebellum	SCAN
rs1728232	AMPD1	cis	parietal	SCAN
rs1728232	DENND2C	cis	parietal	SCAN
rs1728232	OVGP1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113535800-113568800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:113541000-113573800	Weak transcription	Right Ventricle	heart
3	chr1:113543200-113574400	Weak transcription	HSMM	muscle
4	chr1:113551200-113569800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:113551200-113569800	Weak transcription	Left Ventricle	heart
6	chr1:113552800-113570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:113553000-113572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:113555600-113572200	Weak transcription	Primary T cells from cord blood	blood
9	chr1:113555600-113584200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:113562400-113574000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:113563400-113564800	Enhancers	Stomach Mucosa	stomach
12	chr1:113563800-113564800	Enhancers	Fetal Heart	heart
13	chr1:113564000-113564800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:113564000-113564800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:113564000-113564800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:113564000-113564800	Enhancers	K562	blood
17	chr1:113564000-113565000	Enhancers	Liver	Liver
18	chr1:113564000-113569600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:113564200-113564800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:113564200-113564800	Enhancers	Brain Germinal Matrix	brain
21	chr1:113564200-113564800	Enhancers	Osteobl	bone
22	chr1:113564400-113569000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:113564600-113564800	Flanking Active TSS	NHEK	skin
24	chr1:113564600-113565000	Enhancers	HepG2	liver
25	chr1:113564600-113569000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:113564600-113569000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:113564600-113569000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:113564600-113569000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:113564600-113569000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:113564600-113569200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:113564600-113569200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:113564600-113569600	Weak transcription	Placenta	Placenta
33	chr1:113564600-113569800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:113564600-113569800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:113564600-113570000	Weak transcription	Fetal Intestine Small	intestine
36	chr1:113564600-113577600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:113564600-113577600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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