Variant report

Variant	rs61813286
Chromosome Location	chr1:155948645-155948646
allele	C/G
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	CTCF	chr1:155948427-155948650	GM19238	blood:	n/a	chr1:155948539-155948552
3	POLR2A	chr1:155947677-155949686	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:155946498-155950066	GM19099	blood:	n/a	n/a
5	GTF2F1	chr1:155948200-155949218	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:155948113-155949329	K562	blood:	n/a	n/a
7	CTCF	chr1:155948500-155948650	HPAF	blood vessel:	n/a	chr1:155948539-155948552
8	ELK1	chr1:155948623-155948771	K562	blood:	n/a	n/a
9	ZEB1	chr1:155948182-155948669	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:155945717-155950149	K562	blood:	n/a	n/a
11	REST	chr1:155944316-155949059	H1-neurons	neurons:	n/a	chr1:155948423-155948436 chr1:155947302-155947315 chr1:155948473-155948486 chr1:155947032-155947040 chr1:155948493-155948506
12	BHLHE40	chr1:155947849-155948645	GM12878	blood:	n/a	chr1:155948537-155948553
13	CTCF	chr1:155948520-155948670	SAEC	small airway:	n/a	chr1:155948539-155948552
14	MYC	chr1:155948027-155949179	K562	blood:	n/a	n/a
15	CTCF	chr1:155948500-155948650	GM12870	blood:	n/a	chr1:155948539-155948552
16	RELA	chr1:155948186-155950143	GM19099	blood:	n/a	n/a
17	ZBTB7A	chr1:155948021-155948978	K562	blood:	n/a	n/a
18	TBP	chr1:155948185-155949098	H1-hESC	embryonic stem cell:	n/a	n/a
19	SMARCB1	chr1:155946884-155949108	Hela-S3	cervix:	n/a	n/a
20	RAD21	chr1:155948385-155948713	HepG2	liver:	n/a	chr1:155948542-155948552 chr1:155948533-155948547 chr1:155948540-155948553
21	SMARCC1	chr1:155948138-155949474	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:155947477-155950073	GM18526	blood:	n/a	n/a
23	BACH1	chr1:155948303-155948653	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr1:155948054-155948808	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:155948038-155950071	GM12878	blood:	n/a	n/a
26	RCOR1	chr1:155948138-155949065	K562	blood:	n/a	n/a
27	CTCF	chr1:155948560-155948710	NHDF-neo	bronchial:	n/a	n/a
28	CREB1	chr1:155948148-155948792	H1-hESC	embryonic stem cell:	n/a	n/a
29	ELF1	chr1:155948095-155949239	K562	blood:	n/a	n/a
30	POLR2A	chr1:155948033-155948802	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr1:155948520-155948670	AG09309	skin:	n/a	chr1:155948539-155948552
32	PML	chr1:155948096-155948782	K562	blood:	n/a	n/a
33	CTCF	chr1:155948620-155948770	RPTEC	kidney:	n/a	n/a
34	CTCF	chr1:155948500-155948650	GM12866	blood:	n/a	chr1:155948539-155948552
35	MAX	chr1:155947998-155949390	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr1:155948500-155948650	GM12867	blood:	n/a	chr1:155948539-155948552
37	IKZF1	chr1:155948498-155949975	GM12878	blood:	n/a	n/a
38	EGR1	chr1:155948214-155948919	H1-hESC	embryonic stem cell:	n/a	chr1:155948380-155948393 chr1:155948467-155948477 chr1:155948423-155948433 chr1:155948377-155948391
39	ZKSCAN1	chr1:155948143-155948850	Hela-S3	cervix:	n/a	n/a
40	TCF7L2	chr1:155948254-155949030	HCT-116	colon:	n/a	n/a
41	CTBP2	chr1:155948213-155949019	H1-hESC	embryonic stem cell:	n/a	n/a
42	ATF2	chr1:155948303-155948959	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAFK	chr1:155948480-155948905	K562	blood:	n/a	n/a
44	TAF1	chr1:155947629-155948859	K562	blood:	n/a	n/a
45	POLR2A	chr1:155947045-155949602	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:155943560-155949842	HL-60	blood:	n/a	n/a
47	POLR2A	chr1:155946479-155949669	GM12891	blood:	n/a	n/a
48	SIN3AK20	chr1:155948597-155948979	A549	lung:	n/a	n/a
49	TCF12	chr1:155947644-155948843	ECC-1	luminal epithelium:	n/a	n/a
50	FOXM1	chr1:155948061-155949218	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155948081..155949782-chr1:155971306..155973571,2	MCF-7	breast:
2	chr1:155911219..155915431-chr1:155946632..155949866,4	MCF-7	breast:
3	chr1:155946065..155948960-chr1:156022753..156025097,3	MCF-7	breast:
4	chr1:155902613..155905963-chr1:155944776..155950602,8	MCF-7	breast:
5	chr1:155889116..155891316-chr1:155948021..155950216,2	K562	blood:
6	chr1:155902096..155906333-chr1:155944635..155950706,8	K562	blood:
7	chr1:155902752..155906488-chr1:155946119..155948945,5	MCF-7	breast:
8	chr1:155947943..155949602-chr1:155989760..155992633,2	MCF-7	breast:
9	chr1:155946982..155950141-chr1:156022442..156025223,4	MCF-7	breast:
10	chr1:155907837..155914260-chr1:155947632..155952579,11	MCF-7	breast:
11	chr1:155947571..155948767-chr11:62608644..62609651,3	Hela-S3	cervix:
12	chr1:155902760..155905677-chr1:155945999..155951456,7	K562	blood:
13	chr1:155879661..155882760-chr1:155946571..155949454,3	K562	blood:
14	chr1:155947439..155949635-chr1:156095639..156097147,2	MCF-7	breast:
15	chr1:155947462..155948981-chr1:155988389..155991184,2	K562	blood:
16	chr1:155947454..155949209-chr1:155971698..155973677,2	K562	blood:

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000207475	Chromatin interaction
ENSG00000143622	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000116586	Chromatin interaction
ENSG00000160789	Chromatin interaction
ENSG00000163479	Chromatin interaction
ENSG00000116584	Chromatin interaction
ENSG00000132680	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000173080	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10796955	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264422	0.84[ASN][1000 genomes]
rs11264426	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11585845	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1889532	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1889533	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297649	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4661175	0.87[ASN][1000 genomes]
rs4661217	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4661218	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6670493	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534858	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs928596	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61813286	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs61813286	RIT1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155943600-155951400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:155944000-155949200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:155944600-155949400	Active TSS	Aorta	Aorta
4	chr1:155944800-155950000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:155945200-155948800	Active TSS	Fetal Kidney	kidney
6	chr1:155945200-155950800	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr1:155945600-155949000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:155945600-155949000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr1:155945600-155949000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:155945600-155949000	Active TSS	HSMMtube	muscle
11	chr1:155945600-155949200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:155945600-155949200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:155945600-155949200	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr1:155945800-155948800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:155945800-155948800	Active TSS	Ovary	ovary
16	chr1:155945800-155949200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:155945800-155949200	Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:155945800-155949200	Active TSS	Small Intestine	intestine
19	chr1:155946000-155948800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:155946000-155948800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
21	chr1:155946000-155948800	Active TSS	Brain Substantia Nigra	brain
22	chr1:155946000-155948800	Active TSS	Lung	lung
23	chr1:155946000-155949000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:155946000-155949000	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr1:155946000-155949000	Active TSS	Gastric	stomach
26	chr1:155946000-155949600	Active TSS	GM12878-XiMat	blood
27	chr1:155946200-155948800	Active TSS	Primary B cells from peripheral blood	blood
28	chr1:155946200-155949000	Active TSS	NHDF-Ad	bronchial
29	chr1:155946400-155949400	Active TSS	Right Atrium	heart
30	chr1:155947000-155948800	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr1:155947000-155949000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:155947000-155949000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:155947200-155948800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:155947200-155948800	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:155947200-155948800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr1:155947200-155948800	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr1:155947200-155948800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:155947200-155948800	Active TSS	Fetal Lung	lung
39	chr1:155947200-155948800	Active TSS	HMEC	breast
40	chr1:155947200-155949000	Active TSS	H1 Cell Line	embryonic stem cell
41	chr1:155947200-155949000	Active TSS	Spleen	Spleen
42	chr1:155947200-155949000	Active TSS	A549	lung
43	chr1:155947200-155949200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr1:155947200-155949400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:155947400-155948800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:155947400-155948800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:155947400-155948800	Active TSS	Colon Smooth Muscle	Colon
48	chr1:155947400-155948800	Active TSS	Fetal Heart	heart
49	chr1:155947400-155948800	Active TSS	Fetal Intestine Large	intestine
50	chr1:155947400-155948800	Active TSS	Fetal Intestine Small	intestine

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