Variant report

Variant	rs7534858
Chromosome Location	chr1:155946399-155946400
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155945649-155950249	K562	blood:	n/a	n/a
2	POLR2A	chr1:155946253-155947842	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr1:155945717-155950149	K562	blood:	n/a	n/a
4	REST	chr1:155944316-155949059	H1-neurons	neurons:	n/a	chr1:155948423-155948436 chr1:155947302-155947315 chr1:155948473-155948486 chr1:155947032-155947040 chr1:155948493-155948506
5	WRNIP1	chr1:155944973-155947896	GM12878	blood:	n/a	n/a
6	SRF	chr1:155946357-155946572	GM12878	blood:	n/a	chr1:155946455-155946473
7	MXI1	chr1:155945871-155947195	GM12878	blood:	n/a	n/a
8	SPI1	chr1:155945486-155946626	HL-60	blood:	n/a	chr1:155945900-155945913 chr1:155946052-155946065
9	POU2F2	chr1:155946237-155946925	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:155946079-155946817	K562	blood:	n/a	n/a
11	JUND	chr1:155945772-155946699	K562	blood:	n/a	chr1:155946505-155946514
12	POLR2A	chr1:155946158-155947423	PBDE	blood:	n/a	n/a
13	UBTF	chr1:155946041-155946778	K562	blood:	n/a	n/a
14	POLR2A	chr1:155943560-155949842	HL-60	blood:	n/a	n/a
15	MYBL2	chr1:155946245-155946597	HepG2	liver:	n/a	n/a
16	RUNX3	chr1:155945753-155946980	GM12878	blood:	n/a	chr1:155946483-155946492 chr1:155946483-155946492
17	CHD2	chr1:155945745-155946790	Hela-S3	cervix:	n/a	chr1:155946050-155946060
18	MAZ	chr1:155944495-155949843	IMR90	lung:	n/a	chr1:155944774-155944784 chr1:155945544-155945554
19	SIN3AK20	chr1:155946387-155946785	K562	blood:	n/a	n/a
20	EP300	chr1:155946377-155946523	K562	blood:	n/a	n/a
21	NFIC	chr1:155945718-155946879	ECC-1	luminal epithelium:	n/a	chr1:155946079-155946096 chr1:155946079-155946095 chr1:155946079-155946107 chr1:155946513-155946529
22	TAF1	chr1:155946387-155946845	GM12878	blood:	n/a	n/a
23	STAT5A	chr1:155945377-155950185	GM12878	blood:	n/a	chr1:155946053-155946065 chr1:155946051-155946063 chr1:155949809-155949817 chr1:155949268-155949276 chr1:155946455-155946466 chr1:155948325-155948332 chr1:155947672-155947684 chr1:155946644-155946656 chr1:155945901-155945913 chr1:155947305-155947317
24	RELA	chr1:155945949-155946690	GM19193	blood:	n/a	n/a
25	CHD2	chr1:155945825-155946530	GM12878	blood:	n/a	chr1:155946050-155946060
26	SRF	chr1:155946275-155946609	K562	blood:	n/a	chr1:155946455-155946473
27	POLR2A	chr1:155945399-155950018	SK-N-MC	brain:	n/a	n/a
28	RELA	chr1:155945954-155946675	GM19099	blood:	n/a	n/a
29	EP300	chr1:155946027-155946700	GM12878	blood:	n/a	chr1:155946551-155946561
30	POLR2A	chr1:155945767-155946736	K562	blood:	n/a	n/a
31	PML	chr1:155945376-155946919	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:155946273-155950193	GM18505	blood:	n/a	n/a
33	IKZF1	chr1:155945599-155946792	GM12878	blood:	n/a	chr1:155945630-155945638
34	EP300	chr1:155946003-155946555	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:155945870-155950163	GM12878	blood:	n/a	n/a
36	NFATC1	chr1:155945673-155946561	GM12878	blood:	n/a	n/a
37	MAX	chr1:155945761-155946710	NB4	blood:	n/a	n/a
38	SRF	chr1:155946274-155946553	GM12878	blood:	n/a	chr1:155946455-155946473
39	RCOR1	chr1:155945925-155946452	GM12878	blood:	n/a	n/a
40	NFATC1	chr1:155946244-155946825	GM12878	blood:	n/a	n/a
41	REST	chr1:155946295-155947172	HL-60	blood:	n/a	chr1:155947032-155947040
42	POLR2A	chr1:155945739-155946780	SK-N-MC	brain:	n/a	n/a
43	EGR1	chr1:155946050-155946650	K562	blood:	n/a	chr1:155946504-155946514 chr1:155946503-155946513 chr1:155946499-155946512 chr1:155946390-155946400 chr1:155946194-155946208 chr1:155946196-155946211
44	RUNX3	chr1:155945780-155949781	GM12878	blood:	n/a	chr1:155946483-155946492 chr1:155946483-155946492
45	UBTF	chr1:155946368-155946704	K562	blood:	n/a	n/a
46	MAZ	chr1:155945697-155946663	GM12878	blood:	n/a	n/a
47	NFIC	chr1:155945993-155946736	GM12878	blood:	n/a	chr1:155946079-155946096 chr1:155946079-155946095 chr1:155946079-155946107 chr1:155946513-155946529
48	NFIC	chr1:155945807-155946994	GM12878	blood:	n/a	chr1:155946079-155946096 chr1:155946079-155946095 chr1:155946079-155946107 chr1:155946513-155946529
49	NR2F2	chr1:155945617-155946815	K562	blood:	n/a	n/a
50	POLR2A	chr1:155945756-155948033	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155946065..155948960-chr1:156022753..156025097,3	MCF-7	breast:
2	chr1:155902613..155905963-chr1:155944776..155950602,8	MCF-7	breast:
3	chr1:155902096..155906333-chr1:155944635..155950706,8	K562	blood:
4	chr1:155916376..155918441-chr1:155945266..155947635,3	K562	blood:
5	chr1:155902752..155906488-chr1:155946119..155948945,5	MCF-7	breast:
6	chr1:155945057..155948418-chr1:156022747..156026553,6	K562	blood:
7	chr1:155908945..155912358-chr1:155944278..155947594,3	MCF-7	breast:
8	chr1:155946078..155947877-chr1:155959133..155960966,2	MCF-7	breast:
9	chr1:155902760..155905677-chr1:155945999..155951456,7	K562	blood:
10	chr1:155945057..155948418-chr1:156022741..156026553,6	K562	blood:
11	chr1:155944822..155946869-chr1:155964888..155967395,2	MCF-7	breast:
12	chr1:155944622..155946767-chr1:156092062..156094362,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273002	TF binding region
ARHGEF2	TF binding region
ENSG00000116584	Chromatin interaction
ENSG00000132680	Chromatin interaction
ENSG00000173080	Chromatin interaction
ENSG00000160789	Chromatin interaction
ENSG00000116586	Chromatin interaction
ENSG00000160803	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10796955	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1111102	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs11264426	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585845	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12037177	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs12080846	0.89[ASN][1000 genomes]
rs12091273	0.89[ASN][1000 genomes]
rs12091361	0.89[ASN][1000 genomes]
rs12118795	0.90[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs12568523	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs1889532	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1889533	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2016251	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs2282301	0.95[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2297649	0.95[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2364403	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs4661175	0.86[ASW][hapmap]
rs4661217	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4661218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61813286	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6427297	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs6667652	0.95[CEU][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs6670493	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6696019	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs729022	0.82[MEX][hapmap]
rs867549	0.95[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs867550	0.95[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs915178	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs915181	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs928596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7534858	SPRR3	cis	parietal	SCAN
rs7534858	ROBLD3	cis	parietal	SCAN
rs7534858	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs7534858	RIT1	cis	cerebellum	SCAN
rs7534858	PRUNE	cis	cerebellum	SCAN
rs7534858	YY1AP1	cis	cerebellum	SCAN
rs7534858	RIT1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155943000-155947400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:155943600-155947200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:155943600-155951400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:155944000-155946800	Enhancers	Stomach Mucosa	stomach
5	chr1:155944000-155947200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:155944000-155947600	Flanking Active TSS	Brain Anterior Caudate	brain
7	chr1:155944000-155947600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr1:155944000-155947800	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr1:155944000-155949200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:155944200-155947400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:155944200-155947600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr1:155944200-155947800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:155944200-155947800	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr1:155944400-155946400	Flanking Active TSS	Right Atrium	heart
15	chr1:155944400-155947200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:155944400-155947400	Flanking Active TSS	NH-A	brain
17	chr1:155944400-155947600	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr1:155944600-155947200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:155944600-155947400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:155944600-155947400	Flanking Active TSS	Right Ventricle	heart
21	chr1:155944600-155949400	Active TSS	Aorta	Aorta
22	chr1:155944800-155947400	Flanking Active TSS	Fetal Heart	heart
23	chr1:155944800-155947400	Flanking Active TSS	Hela-S3	cervix
24	chr1:155944800-155947400	Flanking Active TSS	HUVEC	blood vessel
25	chr1:155944800-155950000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:155945000-155946400	Flanking Active TSS	HepG2	liver
27	chr1:155945000-155947200	Flanking Active TSS	A549	lung
28	chr1:155945000-155947400	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr1:155945000-155947400	Flanking Active TSS	Left Ventricle	heart
30	chr1:155945000-155947600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:155945200-155946800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:155945200-155947000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:155945200-155947000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr1:155945200-155947400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:155945200-155947600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:155945200-155948600	Active TSS	Fetal Brain Female	brain
37	chr1:155945200-155948800	Active TSS	Fetal Kidney	kidney
38	chr1:155945200-155950800	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr1:155945400-155947400	Flanking Active TSS	Fetal Intestine Large	intestine
40	chr1:155945400-155947400	Flanking Active TSS	Placenta	Placenta
41	chr1:155945400-155947400	Flanking Active TSS	Dnd41	blood
42	chr1:155945400-155948600	Active TSS	Thymus	Thymus
43	chr1:155945600-155946400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:155945600-155946800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:155945600-155947000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:155945600-155947000	Active TSS	NHLF	lung
47	chr1:155945600-155947600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:155945600-155947600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:155945600-155948600	Active TSS	Brain Angular Gyrus	brain
50	chr1:155945600-155949000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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