Variant report

Variant	rs10864453
Chromosome Location	chr1:10407169-10407170
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	chr1:10402867..10406209-chr1:10406745..10409622,3	K562	blood:
2	chr1:10400783..10405636-chr1:10406745..10410852,7	K562	blood:

Variant related genes	Relation type
ENSG00000054523	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1002076	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1013952	0.84[ASN][1000 genomes]
rs1013953	0.86[ASN][1000 genomes]
rs10492969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10492971	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10492972	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10492973	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1065828	0.90[ASN][1000 genomes]
rs10864449	0.84[ASN][1000 genomes]
rs10864450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11121537	0.88[ASN][1000 genomes]
rs11121539	0.94[ASN][1000 genomes]
rs11121541	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11121545	0.93[ASN][1000 genomes]
rs11121551	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11121555	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11121557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11121561	0.90[EUR][1000 genomes]
rs11121563	0.80[EUR][1000 genomes]
rs11121566	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11576459	0.86[ASN][1000 genomes]
rs11579365	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11580789	0.86[ASN][1000 genomes]
rs11580854	0.83[ASN][1000 genomes]
rs11582123	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11584023	0.84[ASN][1000 genomes]
rs11585794	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs11587309	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11587495	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs12117635	0.84[ASN][1000 genomes]
rs12120042	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12120191	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12122029	0.86[ASN][1000 genomes]
rs12125535	0.87[ASN][1000 genomes]
rs12127604	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12128374	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12130563	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12131441	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12132134	0.93[ASN][1000 genomes]
rs12133617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12136404	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12137880	0.94[ASN][1000 genomes]
rs12139981	0.94[ASN][1000 genomes]
rs12141246	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12141416	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12402723	0.83[EUR][1000 genomes]
rs12403465	0.93[ASN][1000 genomes]
rs12406943	0.84[ASN][1000 genomes]
rs12409137	0.84[ASN][1000 genomes]
rs12409754	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12409933	0.91[ASN][1000 genomes]
rs12722830	0.96[ASN][1000 genomes]
rs12725210	0.93[ASN][1000 genomes]
rs12737239	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12738317	0.91[ASN][1000 genomes]
rs12753426	0.91[ASN][1000 genomes]
rs12757288	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1467653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1538557	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1555849	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1556915	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs1556916	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1556917	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17034643	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17034821	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17396973	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17402762	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17410217	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1970379	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2027330	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2039778	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2105212	0.83[ASN][1000 genomes]
rs2148152	0.90[ASN][1000 genomes]
rs2182326	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2185252	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2276100	0.96[ASN][1000 genomes]
rs34565762	0.84[ASN][1000 genomes]
rs34636442	0.88[ASN][1000 genomes]
rs35388505	0.93[ASN][1000 genomes]
rs35811280	0.91[EUR][1000 genomes]
rs35850116	0.84[ASN][1000 genomes]
rs3737155	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3748575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3748577	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3748579	0.91[ASN][1000 genomes]
rs3748581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3762288	0.90[EUR][1000 genomes]
rs4240911	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4333852	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4475756	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4529713	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4623	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4845930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845931	0.86[ASN][1000 genomes]
rs4845932	0.84[ASN][1000 genomes]
rs4846197	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4846198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4846199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4846205	0.84[ASN][1000 genomes]
rs4846206	0.84[ASN][1000 genomes]
rs4846207	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4846209	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4846211	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4846212	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4846213	0.97[ASN][1000 genomes]
rs4846216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4846218	0.90[EUR][1000 genomes]
rs4846219	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4846221	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs55676616	0.83[ASN][1000 genomes]
rs58014725	0.85[EUR][1000 genomes]
rs61326491	0.88[ASN][1000 genomes]
rs61775885	0.83[ASN][1000 genomes]
rs61775887	0.83[ASN][1000 genomes]
rs61778376	0.96[ASN][1000 genomes]
rs61778399	0.90[ASN][1000 genomes]
rs61778401	0.90[ASN][1000 genomes]
rs61778402	0.90[ASN][1000 genomes]
rs61778403	0.87[ASN][1000 genomes]
rs61778404	0.83[ASN][1000 genomes]
rs6541084	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6541085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6541089	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6541090	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541094	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs6661326	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs6674949	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6682868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6685895	0.84[ASN][1000 genomes]
rs6696056	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7368073	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7418410	0.88[CEU][hapmap]
rs746881	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7524693	0.87[ASN][1000 genomes]
rs7524908	0.86[ASN][1000 genomes]
rs7546364	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7546368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7547513	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7553228	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7553935	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs912961	0.88[ASN][1000 genomes]
rs912962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs912963	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9332414	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs946501	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs946502	0.84[ASN][1000 genomes]
rs946503	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs946504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10864453	PGD	Cis_1M	lymphoblastoid	RTeQTL
rs10864453	PGD	cis	multi-tissue	Pritchard
rs10864453	PGD	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10364600-10431000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:10380400-10436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:10380600-10426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:10381000-10436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:10385200-10436400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:10386000-10434800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:10386400-10421600	Weak transcription	Hela-S3	cervix
8	chr1:10386800-10408600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:10393200-10415800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:10393200-10431200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:10393600-10430800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:10393800-10444600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:10394200-10409800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:10394200-10410000	Strong transcription	Fetal Brain Female	brain
15	chr1:10394200-10410000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr1:10394200-10411400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:10394200-10413200	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:10394200-10414200	Strong transcription	Brain Germinal Matrix	brain
19	chr1:10394200-10414200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr1:10394200-10415800	Strong transcription	Adipose Nuclei	Adipose
21	chr1:10394200-10415800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr1:10394200-10441800	Strong transcription	Liver	Liver
23	chr1:10394400-10409400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:10394400-10410000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr1:10394400-10411200	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:10394400-10411400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:10394400-10413400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:10394400-10414200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:10395600-10408400	Weak transcription	Small Intestine	intestine
30	chr1:10395600-10425200	Weak transcription	Thymus	Thymus
31	chr1:10396400-10409400	Strong transcription	HepG2	liver
32	chr1:10397600-10421000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:10397800-10407400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:10397800-10408400	Weak transcription	Fetal Thymus	thymus
35	chr1:10397800-10410600	Weak transcription	Right Ventricle	heart
36	chr1:10397800-10425400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:10397800-10434800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:10398000-10421000	Weak transcription	NHEK	skin
39	chr1:10398000-10438000	Weak transcription	GM12878-XiMat	blood
40	chr1:10398400-10425400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:10399000-10420800	Weak transcription	NHLF	lung
42	chr1:10400000-10407200	Strong transcription	Fetal Intestine Large	intestine
43	chr1:10400000-10410000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:10400000-10416200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:10400200-10407200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:10400200-10407400	Weak transcription	HMEC	breast
47	chr1:10400200-10409400	Strong transcription	HSMM	muscle
48	chr1:10400200-10413600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:10400200-10438200	Weak transcription	Stomach Mucosa	stomach
50	chr1:10400600-10434600	Weak transcription	K562	blood

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