Variant report

Variant	rs639692
Chromosome Location	chr3:42643425-42643426
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr3:42643359-42643678	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUN	chr3:42642947-42644000	K562	blood:	n/a	n/a
3	POLR2A	chr3:42641593-42644059	K562	blood:	n/a	n/a
4	CTCF	chr3:42643420-42643570	HAc	cerebellar:	n/a	n/a
5	CHD1	chr3:42642636-42643554	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:42643420-42643570	GM12871	blood:	n/a	n/a
7	TEAD4	chr3:42641408-42644046	K562	blood:	n/a	n/a
8	BHLHE40	chr3:42643417-42643692	K562	blood:	n/a	n/a
9	STAT3	chr3:42643165-42644091	MCF10A-Er-Src	breast:	n/a	n/a
10	UBTF	chr3:42643399-42643761	K562	blood:	n/a	n/a
11	RAD21	chr3:42643424-42643759	HepG2	liver:	n/a	n/a
12	CTCF	chr3:42643420-42643570	GM12865	blood:	n/a	n/a
13	MYC	chr3:42643374-42644033	MCF10A-Er-Src	breast:	n/a	n/a
14	EP300	chr3:42642568-42643731	K562	blood:	n/a	n/a
15	POLR2A	chr3:42643374-42643909	MCF10A-Er-Src	breast:	n/a	n/a
16	TEAD4	chr3:42643190-42643985	K562	blood:	n/a	n/a
17	RUNX3	chr3:42643346-42643761	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:42641419-42643594	GM12891	blood:	n/a	n/a
19	ARID3A	chr3:42642770-42644222	K562	blood:	n/a	n/a
20	CTCF	chr3:42643375-42643769	K562	blood:	n/a	n/a
21	CTCF	chr3:42643380-42643530	GM12870	blood:	n/a	n/a
22	CTCF	chr3:42643340-42643490	A549	lung:	n/a	n/a
23	CTCF	chr3:42643409-42643741	K562	blood:	n/a	n/a
24	CTCF	chr3:42643404-42643780	GM12878	blood:	n/a	n/a
25	RAD21	chr3:42643402-42643783	H1-hESC	embryonic stem cell:	n/a	n/a
26	REST	chr3:42641257-42643965	H1-neurons	neurons:	n/a	chr3:42641841-42641848
27	IRF1	chr3:42641270-42643993	K562	blood:	n/a	chr3:42641807-42641819 chr3:42641804-42641818 chr3:42641829-42641838

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
2	chr3:42640361..42643591-chr3:42693270..42696162,5	K562	blood:
3	chr3:42509273..42511295-chr3:42641295..42643446,2	MCF-7	breast:
4	chr3:42604560..42606277-chr3:42641170..42643967,2	K562	blood:
5	chr3:42640678..42643591-chr3:42694568..42696079,2	K562	blood:
6	chr3:42621283..42625330-chr3:42639303..42643596,7	MCF-7	breast:
7	chr3:42604086..42606277-chr3:42642467..42644274,2	K562	blood:
8	chr3:42639395..42643636-chr3:42699754..42702498,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SS18L2-2	chr3:42642476-42644548	NONHSAT089241

No data

Variant related genes	Relation type
SEC22C	TF binding region
ENSG00000230084	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000235787	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs2136012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271181	0.85[EUR][1000 genomes]
rs2271185	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271186	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2976533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339723	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs339725	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339727	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339728	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs339733	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342507	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs342508	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs342521	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs342522	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342536	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342537	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774398	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4549	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs586082	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587712	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597498	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs607568	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612733	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614323	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs617722	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627664	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638836	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441892	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs663673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs704979	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8351	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs925457	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9865109	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs639692	TMEM42	cis	cerebellum	SCAN
rs639692	NKTR	cis	Nerve Tibial	GTEx
rs639692	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs639692	NKTR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42640800-42643600	Active TSS	Hela-S3	cervix
2	chr3:42640800-42643800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:42641000-42643600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:42641200-42643600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:42641200-42643600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:42641200-42643600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:42641200-42643600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:42641200-42643600	Active TSS	Fetal Intestine Large	intestine
9	chr3:42641200-42643600	Active TSS	Fetal Muscle Trunk	muscle
10	chr3:42641200-42643600	Active TSS	K562	blood
11	chr3:42641200-42643800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr3:42641200-42643800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:42641200-42643800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:42641200-42643800	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:42641200-42643800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:42641200-42643800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:42641200-42643800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:42641200-42643800	Active TSS	Fetal Intestine Small	intestine
19	chr3:42641200-42643800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:42641200-42643800	Active TSS	A549	lung
21	chr3:42641200-42643800	Active TSS	HSMMtube	muscle
22	chr3:42641200-42643800	Active TSS	NHLF	lung
23	chr3:42641200-42644000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:42641200-42644000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:42641200-42644000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:42641200-42644200	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:42641200-42644200	Active TSS	HMEC	breast
28	chr3:42641400-42643600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:42641400-42643600	Active TSS	Ovary	ovary
30	chr3:42641400-42643600	Active TSS	GM12878-XiMat	blood
31	chr3:42641400-42643600	Active TSS	NHDF-Ad	bronchial
32	chr3:42641400-42643800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr3:42641400-42643800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:42641400-42643800	Active TSS	H9 Cell Line	embryonic stem cell
35	chr3:42641400-42643800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:42641400-42643800	Active TSS	Psoas Muscle	Psoas
37	chr3:42641400-42643800	Active TSS	Right Ventricle	heart
38	chr3:42641400-42644000	Active TSS	Left Ventricle	heart
39	chr3:42641600-42643600	Active TSS	HSMM	muscle
40	chr3:42642200-42643600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:42642200-42644000	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr3:42642600-42643800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr3:42642600-42644000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:42642800-42643800	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr3:42642800-42643800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:42642800-42643800	Active TSS	Right Atrium	heart
47	chr3:42642800-42644000	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr3:42642800-42644000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:42642800-42644000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr3:42642800-42644000	Flanking Active TSS	Brain Hippocampus Middle	brain

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