Variant report

Variant	rs3013431
Chromosome Location	chr1:113242488-113242489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113242406-113244648	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:113240102-113248907	U87	brain:	n/a	n/a
3	POLR2A	chr1:113242434-113242498	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:113242446-113242674	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:113242402-113245857	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:113240738-113245862	K562	blood:	n/a	n/a
7	POLR2A	chr1:113240207-113248892	K562	blood:	n/a	n/a
8	POLR2A	chr1:113241110-113248218	K562	blood:	n/a	n/a
9	POLR2A	chr1:113240680-113249021	K562	blood:	n/a	n/a
10	POLR2A	chr1:113242313-113244687	K562	blood:	n/a	n/a
11	POLR2A	chr1:113241223-113246166	K562	blood:	n/a	n/a
12	HEY1	chr1:113242133-113244405	K562	blood:	n/a	n/a
13	POLR2A	chr1:113240211-113248533	A549	lung:	n/a	n/a
14	POLR2A	chr1:113240649-113246839	K562	blood:	n/a	n/a
15	POLR2A	chr1:113242428-113242618	HepG2	liver:	n/a	n/a
16	NR2F2	chr1:113241916-113244347	K562	blood:	n/a	n/a
17	POLR2A	chr1:113240403-113244696	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:113240166-113244996	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr1:113241207-113246146	K562	blood:	n/a	n/a
20	POLR2A	chr1:113242397-113245876	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr1:113241038-113244807	K562	blood:	n/a	n/a
22	POLR2A	chr1:113240885-113246230	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr1:113240375-113248999	K562	blood:	n/a	n/a
24	JUN	chr1:113240870-113245032	K562	blood:	n/a	chr1:113243606-113243619
25	TEAD4	chr1:113241031-113244470	K562	blood:	n/a	n/a
26	POLR2A	chr1:113241165-113248430	GM12891	blood:	n/a	n/a
27	BHLHE40	chr1:113242164-113242545	K562	blood:	n/a	n/a
28	POLR2A	chr1:113241990-113242812	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:113241914-113246120	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:113240783-113246836	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr1:113241090-113246187	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr1:113242486-113242639	MCF-7	breast:	n/a	n/a
33	POLR2A	chr1:113240610-113244540	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:113240176-113246017	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr1:113242005-113242615	GM12892	blood:	n/a	n/a
36	POLR2A	chr1:113241379-113242714	K562	blood:	n/a	n/a
37	POLR2A	chr1:113241768-113248472	U87	brain:	n/a	n/a
38	POLR2A	chr1:113240249-113248607	HepG2	liver:	n/a	n/a
39	POLR2A	chr1:113242062-113248544	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr1:113241052-113245981	K562	blood:	n/a	n/a
41	MAZ	chr1:113242132-113243876	IMR90	lung:	n/a	n/a
42	POLR2A	chr1:113240102-113248913	U87	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
2	chr1:113160443..113165363-chr1:113242054..113245654,5	K562	blood:
3	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
4	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
5	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
6	chr1:112937481..112939065-chr1:113242426..113245199,2	MCF-7	breast:
7	chr1:112937855..112940278-chr1:113239914..113242532,2	MCF-7	breast:
8	chr1:113240296..113243095-chr1:113496225..113498995,2	K562	blood:
9	chr1:113215224..113219998-chr1:113238829..113244717,20	MCF-7	breast:
10	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
11	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225075	TF binding region
ENSG00000155363	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000271810	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000235299	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12046329	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12046466	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1994604	0.83[ASN][1000 genomes]
rs2932532	0.97[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2932536	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2999154	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2999155	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2999157	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3013439	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3013440	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3103450	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6691932	0.80[ASN][1000 genomes]
rs6700673	0.83[ASN][1000 genomes]
rs7415820	0.83[ASN][1000 genomes]
rs7524494	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7546094	0.83[ASN][1000 genomes]
rs902289	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	esv997362	chr1:113234820-113243297	Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3013431	ST7L	cis	Adipose Subcutaneous	GTEx
rs3013431	ST7L	cis	lung	GTEx
rs3013431	ST7L	cis	Thyroid	GTEx
rs3013431	ST7L	cis	multi-tissue	Pritchard
rs3013431	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs3013431	ST7L	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
2	chr1:113222000-113243000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:113228600-113242800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:113228600-113242800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:113229600-113243200	Strong transcription	Dnd41	blood
7	chr1:113230200-113242600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:113230200-113243000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:113230200-113243200	Strong transcription	Primary T cells from cord blood	blood
10	chr1:113230600-113242600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr1:113231600-113243000	Weak transcription	Psoas Muscle	Psoas
12	chr1:113231600-113243200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:113231800-113242600	Strong transcription	Fetal Lung	lung
14	chr1:113232000-113242600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:113232400-113242600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:113234000-113242800	Strong transcription	Brain Anterior Caudate	brain
17	chr1:113234000-113244400	Strong transcription	Thymus	Thymus
18	chr1:113234200-113242600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:113234200-113242800	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr1:113234400-113242800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:113235800-113244600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:113237200-113243400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:113237200-113243400	Strong transcription	Brain Germinal Matrix	brain
24	chr1:113238000-113246400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:113238400-113243200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:113238400-113243600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:113238800-113246600	Genic enhancers	Placenta Amnion	Placenta Amnion
28	chr1:113239400-113243000	Weak transcription	Brain Angular Gyrus	brain
29	chr1:113239400-113246600	Genic enhancers	Fetal Intestine Large	intestine
30	chr1:113239600-113242600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:113239600-113242800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:113239600-113242800	Weak transcription	Brain Substantia Nigra	brain
33	chr1:113240200-113243800	Enhancers	Fetal Heart	heart
34	chr1:113240400-113247000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:113240400-113247200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:113240600-113242600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
37	chr1:113240600-113243200	Genic enhancers	H1 Cell Line	embryonic stem cell
38	chr1:113240600-113243200	Genic enhancers	HSMMtube	muscle
39	chr1:113240600-113244600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:113240600-113245600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:113240600-113245800	Genic enhancers	Lung	lung
42	chr1:113240600-113246800	Genic enhancers	Colonic Mucosa	Colon
43	chr1:113240600-113247000	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr1:113240600-113247000	Genic enhancers	Fetal Muscle Leg	muscle
45	chr1:113240600-113247200	Genic enhancers	Placenta	Placenta
46	chr1:113240800-113243000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:113240800-113243400	Enhancers	Right Atrium	heart
48	chr1:113240800-113244400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
49	chr1:113240800-113244600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
50	chr1:113240800-113246400	Genic enhancers	Pancreas	Pancrea

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