Variant report

Variant	rs12042903
Chromosome Location	chr1:45966298-45966299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr1:45965477-45966308	K562	blood:	n/a	n/a
2	IRF4	chr1:45965536-45966325	GM12878	blood:	n/a	n/a
3	YY1	chr1:45965463-45966306	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr1:45965342-45966340	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr1:45965325-45966325	HL-60	blood:	n/a	n/a
6	CEBPB	chr1:45965469-45966636	HepG2	liver:	n/a	chr1:45966124-45966132
7	REST	chr1:45965144-45966351	H1-neurons	neurons:	n/a	n/a
8	ZNF384	chr1:45965683-45966769	GM12878	blood:	n/a	n/a
9	SP1	chr1:45965222-45966316	HCT-116	colon:	n/a	n/a
10	YY1	chr1:45965452-45966306	GM12878	blood:	n/a	n/a
11	HCFC1	chr1:45964803-45966980	Hela-S3	cervix:	n/a	n/a
12	MTA3	chr1:45965191-45966319	GM12878	blood:	n/a	n/a
13	MAX	chr1:45965436-45966357	A549	lung:	n/a	n/a
14	MAX	chr1:45965384-45966329	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr1:45964964-45967174	SK-N-SH	brain:	n/a	n/a
16	E2F6	chr1:45965702-45966318	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:45964582-45967225	HepG2	liver:	n/a	n/a
18	ETS1	chr1:45965354-45966343	K562	blood:	n/a	n/a
19	MTA3	chr1:45964977-45966341	GM12878	blood:	n/a	n/a
20	GABPA	chr1:45965509-45966330	K562	blood:	n/a	n/a
21	POLR2A	chr1:45965218-45966367	SK-N-MC	brain:	n/a	n/a
22	MAX	chr1:45965691-45966300	H1-hESC	embryonic stem cell:	n/a	n/a
23	CREB1	chr1:45965377-45966334	GM12878	blood:	n/a	n/a
24	MAX	chr1:45965406-45966339	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr1:45965055-45966317	K562	blood:	n/a	n/a
26	E2F6	chr1:45965421-45966350	K562	blood:	n/a	n/a
27	TEAD4	chr1:45965248-45966332	K562	blood:	n/a	n/a
28	POLR2A	chr1:45965393-45966315	PANC-1	pancreas:	n/a	n/a
29	CEBPB	chr1:45965401-45966711	Hela-S3	cervix:	n/a	chr1:45966124-45966132
30	MAX	chr1:45965421-45966356	NB4	blood:	n/a	n/a
31	MAX	chr1:45965249-45966300	Hela-S3	cervix:	n/a	n/a
32	TRIM28	chr1:45965577-45966328	K562	blood:	n/a	n/a
33	POLR2A	chr1:45965163-45966336	PFSK-1	brain:	n/a	n/a
34	TAF1	chr1:45965373-45966329	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr1:45965284-45966320	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr1:45965373-45966334	ECC-1	luminal epithelium:	n/a	n/a
37	CREB1	chr1:45965269-45966354	K562	blood:	n/a	n/a
38	STAT5A	chr1:45965175-45966332	GM12878	blood:	n/a	n/a
39	CREB1	chr1:45965284-45966338	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:45964960-45966439	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr1:45965339-45966319	Hela-S3	cervix:	n/a	n/a
42	MYC	chr1:45965527-45966342	K562	blood:	n/a	n/a
43	POLR2A	chr1:45965254-45966349	K562	blood:	n/a	n/a
44	MAX	chr1:45965205-45966342	HepG2	liver:	n/a	n/a
45	YY1	chr1:45965397-45966318	ECC-1	luminal epithelium:	n/a	n/a
46	MAX	chr1:45965189-45966357	HCT-116	colon:	n/a	n/a
47	YY1	chr1:45965441-45966332	HepG2	liver:	n/a	n/a
48	PML	chr1:45965365-45966326	GM12878	blood:	n/a	n/a
49	ELF1	chr1:45965491-45966302	GM12878	blood:	n/a	n/a
50	RCOR1	chr1:45965349-45966331	Hela-S3	cervix:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45239737..45242586-chr1:45965500..45967251,2	K562	blood:
2	chr1:45804114..45807301-chr1:45961577..45967419,8	K562	blood:
3	chr1:45966070..45969060-chr1:46033668..46035384,2	MCF-7	breast:
4	chr1:45185969..45188598-chr1:45964540..45967567,4	K562	blood:
5	chr1:45283510..45287262-chr1:45964108..45968951,6	K562	blood:
6	chr1:45952646..45954421-chr1:45965976..45968197,2	K562	blood:
7	chr1:45768003..45772070-chr1:45964648..45967315,5	K562	blood:
8	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
9	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
10	chr1:45965940..45967492-chr1:46038830..46041668,2	K562	blood:
11	chr1:45265558..45267516-chr1:45964222..45967034,2	K562	blood:
12	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
13	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:
14	chr1:45272934..45277358-chr1:45964626..45967668,4	K562	blood:
15	chr1:45284392..45287262-chr1:45964108..45967526,3	K562	blood:
16	chr1:45804471..45806506-chr1:45965051..45967533,2	K562	blood:
17	chr1:45185644..45188958-chr1:45966067..45969348,3	K562	blood:
18	chr1:45965671..45969478-chr1:45972057..45975317,5	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC163P	TF binding region
ENSG00000070759	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000225721	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1006216	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1007858	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10789464	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10890330	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11211111	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11211117	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211118	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211123	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211124	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211128	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12029322	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12037201	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12046816	0.81[EUR][1000 genomes]
rs12066142	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12067642	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12097497	0.81[EUR][1000 genomes]
rs12410493	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12564806	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1494812	0.81[EUR][1000 genomes]
rs1826691	0.81[EUR][1000 genomes]
rs2055145	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2088100	0.81[EUR][1000 genomes]
rs28555082	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2883968	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34673142	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3790582	0.81[EUR][1000 genomes]
rs3790583	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4633317	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660855	0.81[EUR][1000 genomes]
rs4660858	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4660863	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5015340	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55642258	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61788261	0.82[EUR][1000 genomes]
rs61788281	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61788285	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61788336	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61788356	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67683090	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs713358	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7528573	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs868351	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9727262	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9729395	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription 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	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12042903	TESK2	cis	Whole Blood	GTEx
rs12042903	PRDX1	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
2	chr1:45964400-45966600	Active TSS	A549	lung
3	chr1:45964400-45966800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:45964600-45966600	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:45964800-45966600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr1:45964800-45966600	Active TSS	Ovary	ovary
7	chr1:45964800-45967200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:45964800-45967400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:45965000-45966400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:45965000-45966600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:45965000-45966600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:45965000-45966600	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr1:45965000-45966600	Active TSS	Pancreas	Pancrea
14	chr1:45965000-45966800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:45965000-45966800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr1:45965000-45966800	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr1:45965000-45966800	Active TSS	Fetal Kidney	kidney
18	chr1:45965000-45966800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:45965000-45966800	Active TSS	NHLF	lung
20	chr1:45965000-45967000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:45965000-45967000	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr1:45965000-45967200	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr1:45965000-45967200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr1:45965200-45966400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:45965200-45966400	Active TSS	Aorta	Aorta
26	chr1:45965200-45966400	Active TSS	Gastric	stomach
27	chr1:45965200-45966600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:45965200-45966600	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr1:45965200-45966600	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr1:45965200-45966600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr1:45965200-45966600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:45965200-45966600	Active TSS	Psoas Muscle	Psoas
33	chr1:45965200-45966800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:45965200-45966800	Active TSS	Fetal Intestine Large	intestine
35	chr1:45965200-45967000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr1:45965200-45967000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:45965400-45966400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:45965400-45966400	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr1:45965400-45966400	Active TSS	Fetal Heart	heart
40	chr1:45965400-45966400	Active TSS	Lung	lung
41	chr1:45965400-45966400	Active TSS	Spleen	Spleen
42	chr1:45965400-45966400	Active TSS	HSMMtube	muscle
43	chr1:45965400-45966600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:45965400-45966600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:45965400-45966600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:45965400-45966600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:45965400-45966600	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr1:45965400-45966600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:45965400-45966600	Active TSS	Muscle Satellite Cultured Cells	--
50	chr1:45965400-45966600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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