Variant report

Variant	rs2230657
Chromosome Location	chr1:46073489-46073490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46073332-46073803	K562	blood:	n/a	n/a
2	POLR2A	chr1:46072965-46074640	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:46072960-46074725	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:46073334-46074064	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:46073349-46074591	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:46073206-46073730	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr1:46073216-46074546	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:46073418-46073669	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:46073190-46073664	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:46073482-46073605	K562	blood:	n/a	n/a
11	POLR2A	chr1:46073344-46074000	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:46073358-46073529	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:46073315-46073973	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:46073046-46074749	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:46073463-46073504	MCF-7	breast:	n/a	n/a
16	POLR2A	chr1:46072620-46076787	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:46071949-46077053	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:46072597-46073878	K562	blood:	n/a	n/a
19	POLR2A	chr1:46072602-46074693	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46048568..46053199-chr1:46070794..46073826,5	K562	blood:
2	chr1:45986916..45989039-chr1:46073191..46077083,3	K562	blood:

No data

Variant related genes	Relation type
NASP	TF binding region
ENSG00000132780	Chromatin interaction
ENSG00000117450	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10430123	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs10430124	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs10749856	0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.80[ASN][1000 genomes]
rs10789467	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.84[ASN][1000 genomes]
rs10789468	0.83[ASN][1000 genomes]
rs10789470	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10789474	0.81[JPT][hapmap]
rs10890333	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10890334	0.80[YRI][hapmap]
rs10890335	0.80[YRI][hapmap]
rs10890336	0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10890337	0.83[ASN][1000 genomes]
rs10890343	0.83[ASN][1000 genomes]
rs10890344	0.80[ASN][1000 genomes]
rs10890346	0.90[JPT][hapmap]
rs11211151	0.84[ASN][1000 genomes]
rs11211157	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11211158	0.83[ASN][1000 genomes]
rs11211159	0.83[ASN][1000 genomes]
rs11211163	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11211165	0.83[ASN][1000 genomes]
rs11211166	0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs11211178	0.90[JPT][hapmap]
rs11211181	0.85[JPT][hapmap]
rs1135812	0.80[YRI][hapmap]
rs12037459	0.85[CHB][hapmap]
rs12037803	0.83[ASN][1000 genomes]
rs12043945	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs12045096	0.84[ASN][1000 genomes]
rs12049027	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12091503	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1250	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1541131	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1547924	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2050376	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2088102	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs2230658	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2230659	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.91[ASN][1000 genomes]
rs2275085	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs28438704	0.80[ASN][1000 genomes]
rs28442079	0.80[ASN][1000 genomes]
rs28647556	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs28817701	0.95[JPT][hapmap]
rs2934857	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2934859	0.90[JPT][hapmap]
rs2991972	0.90[JPT][hapmap]
rs2991975	0.88[CEU][hapmap]
rs2991977	0.86[ASN][1000 genomes]
rs2991981	0.86[ASN][1000 genomes]
rs2991985	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2991986	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2991987	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs2991989	0.83[YRI][hapmap]
rs2993263	0.90[JPT][hapmap]
rs3013594	0.81[EUR][1000 genomes]
rs3013595	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3013596	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3013597	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3014210	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs3014212	0.86[ASN][1000 genomes]
rs3014216	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs3014218	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3014235	0.80[YRI][hapmap]
rs3014236	0.86[ASN][1000 genomes]
rs3014238	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3014239	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3014242	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs3014243	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3014247	0.80[ASN][1000 genomes]
rs3014251	0.91[ASN][1000 genomes]
rs3811435	0.83[ASN][1000 genomes]
rs4274104	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs4353138	0.80[EUR][1000 genomes]
rs4391704	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs4431884	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4468203	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4559551	0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs4564187	0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.80[ASN][1000 genomes]
rs4607935	0.82[CHB][hapmap]
rs4609469	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.84[ASN][1000 genomes]
rs4626927	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs4660312	0.82[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660879	0.84[ASN][1000 genomes]
rs4660882	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660883	0.85[JPT][hapmap]
rs4660885	0.81[CEU][hapmap]
rs5021934	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs512026	0.85[JPT][hapmap]
rs518216	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs61784796	0.82[ASN][1000 genomes]
rs622798	0.90[JPT][hapmap]
rs6429574	0.83[ASN][1000 genomes]
rs6429575	0.83[ASN][1000 genomes]
rs6429576	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs6656279	0.89[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6665808	0.82[ASN][1000 genomes]
rs6671802	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6690926	0.83[ASN][1000 genomes]
rs6697821	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6699418	0.87[ASN][1000 genomes]
rs6703748	0.80[YRI][hapmap]
rs72688483	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7545118	0.84[ASN][1000 genomes]
rs7547414	0.85[ASN][1000 genomes]
rs8179296	0.83[ASN][1000 genomes]
rs8179402	0.83[ASN][1000 genomes]
rs9793568	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
3	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
5	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
7	nsv945920	chr1:46073152-46073884	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2230657	CCDC163P	cis	Whole Blood	GTEx
rs2230657	MAST2	cis	Artery Tibial	GTEx
rs2230657	CCDC163P	cis	Stomach	GTEx
rs2230657	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs2230657	CCDC163P	cis	Esophagus Muscularis	GTEx
rs2230657	CCDC163P	cis	Heart Left Ventricle	GTEx
rs2230657	MAST2	cis	Artery Aorta	GTEx
rs2230657	GPBP1L1	cis	lung	GTEx
rs2230657	GPBP1L1	cis	Lymphoblastoid	GTEx
rs2230657	CCDC163P	cis	Artery Tibial	GTEx
rs2230657	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs2230657	CCDC163P	cis	lung	GTEx
rs2230657	CCDC163P	cis	Thyroid	GTEx
rs2230657	GPBP1L1	cis	Whole Blood	GTEx
rs2230657	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs2230657	CCDC163P	cis	Esophagus Mucosa	GTEx
rs2230657	Hs.396207	cis	multi-tissue	Pritchard
rs2230657	AKR1A1	cis	Lymphoblastoid	GTEx
rs2230657	AKR1A1	cis	multi-tissue	Pritchard
rs2230657	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs2230657	CCDC163P	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46052000-46081000	Weak transcription	Small Intestine	intestine
2	chr1:46052200-46084200	Weak transcription	Right Atrium	heart
3	chr1:46052400-46080600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:46052800-46078400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:46052800-46081000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:46052800-46086000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:46052800-46089200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:46052800-46099400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:46053600-46086000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:46055000-46085200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:46055200-46090400	Strong transcription	Dnd41	blood
13	chr1:46056000-46079000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:46056800-46074000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:46057400-46081600	Weak transcription	Psoas Muscle	Psoas
16	chr1:46060800-46076200	Weak transcription	Esophagus	oesophagus
17	chr1:46061000-46076200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:46061000-46078800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:46061600-46075200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:46061600-46075200	Weak transcription	Colonic Mucosa	Colon
21	chr1:46062400-46074000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:46062600-46074200	Weak transcription	Brain Anterior Caudate	brain
23	chr1:46066600-46075000	Weak transcription	Fetal Heart	heart
24	chr1:46066800-46084400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:46066800-46086800	Strong transcription	K562	blood
26	chr1:46067000-46086400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:46067200-46086600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:46067200-46087400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:46067400-46086600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:46067600-46077000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:46067600-46077600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:46067800-46076800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr1:46068000-46076800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:46068000-46077000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:46068000-46078800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:46068000-46086600	Strong transcription	Placenta	Placenta
37	chr1:46068200-46076600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:46068200-46085000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:46068200-46086600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:46068200-46087000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:46068200-46087400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr1:46068200-46087400	Strong transcription	Fetal Thymus	thymus
43	chr1:46068400-46074200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:46068800-46076200	Strong transcription	HSMM	muscle
45	chr1:46068800-46078600	Weak transcription	NHLF	lung
46	chr1:46068800-46080800	Weak transcription	NHDF-Ad	bronchial
47	chr1:46069600-46074400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr1:46069600-46074800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:46069600-46077000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:46069800-46073600	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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