Variant report

Variant	rs10191774
Chromosome Location	chr2:55275028-55275029
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	chr2:55274972-55276826	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr2:55274782-55275344	MCF10A-Er-Src	breast:	n/a	n/a
3	UBTF	chr2:55274752-55278735	K562	blood:	n/a	n/a
4	MYC	chr2:55274782-55276825	MCF10A-Er-Src	breast:	n/a	chr2:55276654-55276661 chr2:55274921-55274929 chr2:55276651-55276662
5	CEBPB	chr2:55274930-55275325	A549	lung:	n/a	chr2:55275098-55275109
6	MXI1	chr2:55273915-55275492	IMR90	lung:	n/a	n/a
7	CEBPB	chr2:55274898-55275297	IMR90	lung:	n/a	chr2:55275098-55275109
8	CEBPB	chr2:55275001-55275183	H1-hESC	embryonic stem cell:	n/a	chr2:55275098-55275109
9	STAT3	chr2:55274769-55275252	MCF10A-Er-Src	breast:	n/a	n/a
10	TEAD4	chr2:55274780-55276604	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:55274825-55277952	HL-60	blood:	n/a	n/a
12	BCLAF1	chr2:55274794-55275315	GM12878	blood:	n/a	n/a
13	TCF7L2	chr2:55274866-55275403	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr2:55274966-55278956	Hela-S3	cervix:	n/a	n/a
15	MXI1	chr2:55274845-55276845	Hela-S3	cervix:	n/a	n/a
16	PAX5	chr2:55274933-55275144	GM12878	blood:	n/a	chr2:55275053-55275072
17	FOXA2	chr2:55274988-55275421	HepG2	liver:	n/a	n/a
18	MXI1	chr2:55274609-55279166	SK-N-SH	brain:	n/a	n/a
19	CHD1	chr2:55271552-55280181	IMR90	lung:	n/a	chr2:55276840-55276850
20	POLR2A	chr2:55274804-55275476	HCT-116	colon:	n/a	n/a
21	POLR2A	chr2:55274931-55275531	PANC-1	pancreas:	n/a	n/a
22	CEBPD	chr2:55274967-55275253	HepG2	liver:	n/a	n/a
23	ARID3A	chr2:55274635-55275412	HepG2	liver:	n/a	n/a
24	CEBPB	chr2:55274877-55275347	ECC-1	luminal epithelium:	n/a	chr2:55275098-55275109
25	STAT3	chr2:55274629-55275452	MCF10A-Er-Src	breast:	n/a	n/a
26	TBL1XR1	chr2:55274565-55276771	K562	blood:	n/a	n/a
27	POLR2A	chr2:55274855-55275516	PANC-1	pancreas:	n/a	n/a
28	FOS	chr2:55274689-55275302	MCF10A-Er-Src	breast:	n/a	n/a
29	MYC	chr2:55274905-55276926	NB4	blood:	n/a	chr2:55276654-55276661 chr2:55274921-55274929 chr2:55276651-55276662 chr2:55276832-55276842
30	CEBPB	chr2:55274842-55275452	A549	lung:	n/a	chr2:55275098-55275109
31	PAX5	chr2:55274860-55275273	GM12892	blood:	n/a	chr2:55275053-55275072
32	PML	chr2:55274798-55275445	K562	blood:	n/a	n/a
33	SMC3	chr2:55274981-55278891	Hela-S3	cervix:	n/a	n/a
34	PAX5	chr2:55274812-55275202	GM12891	blood:	n/a	chr2:55275053-55275072
35	RFX5	chr2:55274974-55275390	Hela-S3	cervix:	n/a	n/a
36	PAX5	chr2:55274765-55275377	GM12878	blood:	n/a	chr2:55275053-55275072
37	REST	chr2:55274896-55278466	H1-neurons	neurons:	n/a	chr2:55277989-55277999 chr2:55276641-55276651 chr2:55276185-55276195
38	POLR2A	chr2:55274802-55276973	HepG2	liver:	n/a	n/a
39	POLR2A	chr2:55274608-55278925	K562	blood:	n/a	n/a
40	POLR2A	chr2:55274785-55276919	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr2:55274915-55275247	MCF10A-Er-Src	breast:	n/a	n/a
42	RAD21	chr2:55274683-55278752	IMR90	lung:	n/a	chr2:55277716-55277726
43	CEBPB	chr2:55274893-55276879	Hela-S3	cervix:	n/a	chr2:55275098-55275109
44	CTCF	chr2:55274353-55279779	A549	lung:	n/a	n/a
45	POLR2A	chr2:55274941-55275481	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr2:55274556-55280140	IMR90	lung:	n/a	n/a
47	CEBPB	chr2:55274993-55275231	HepG2	liver:	n/a	chr2:55275098-55275109
48	FOS	chr2:55274759-55275341	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr2:55274490-55275446	U87	brain:	n/a	n/a
50	POLR2A	chr2:55274948-55275147	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55274992..55277411-chr2:55494676..55497816,3	K562	blood:
2	chr2:55273795..55276620-chr2:55843969..55846667,2	K562	blood:
3	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
4	chr2:55240957..55243233-chr2:55273939..55276356,2	K562	blood:
5	chr2:55274992..55276773-chr2:55494676..55496447,2	K562	blood:
6	chr2:54196421..54198197-chr2:55274517..55277399,2	MCF-7	breast:
7	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
8	chr2:55274277..55275806-chr2:55323435..55326407,2	K562	blood:
9	chr2:55274620..55276240-chr2:55348004..55351084,3	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000272606	Chromatin interaction
ENSG00000200086	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000266376	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10170102	0.81[EUR][1000 genomes]
rs10175952	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10180207	0.80[EUR][1000 genomes]
rs10181115	0.81[EUR][1000 genomes]
rs10182203	0.86[EUR][1000 genomes]
rs10191748	0.84[AMR][1000 genomes]
rs10197533	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10206953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10207701	0.87[AMR][1000 genomes]
rs11125554	0.86[EUR][1000 genomes]
rs13387710	0.87[AMR][1000 genomes]
rs13400353	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13401780	0.98[EUR][1000 genomes]
rs13416852	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6545469	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545470	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6744637	0.98[EUR][1000 genomes]
rs6760773	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72912579	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7592869	0.87[AMR][1000 genomes];0.98[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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55259400-55275200	Weak transcription	Esophagus	oesophagus
2	chr2:55271400-55278200	Active TSS	HSMMtube	muscle
3	chr2:55271600-55275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55271600-55275200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:55272600-55275200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr2:55272600-55275400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:55272800-55275600	Transcr. at gene 5' and 3'	HSMM	muscle
9	chr2:55273000-55275600	Transcr. at gene 5' and 3'	Dnd41	blood
10	chr2:55273000-55276200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:55273000-55276800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr2:55273200-55275200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:55273200-55275200	Weak transcription	Gastric	stomach
14	chr2:55273200-55278400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr2:55273200-55278400	Active TSS	GM12878-XiMat	blood
16	chr2:55273400-55275200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:55273400-55275600	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:55273400-55276000	Weak transcription	Spleen	Spleen
19	chr2:55273400-55279800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr2:55273600-55276200	Active TSS	Right Atrium	heart
21	chr2:55273600-55276600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
22	chr2:55273800-55276200	Active TSS	Brain Germinal Matrix	brain
23	chr2:55273800-55278600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr2:55273800-55278600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:55273800-55279000	Active TSS	Psoas Muscle	Psoas
26	chr2:55273800-55279200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:55274000-55275400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:55274000-55275400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr2:55274000-55276200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr2:55274000-55278200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:55274000-55278200	Active TSS	NH-A	brain
32	chr2:55274200-55276200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:55274200-55276400	Active TSS	Fetal Brain Female	brain
34	chr2:55274200-55278400	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:55274200-55278600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:55274200-55278600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:55274200-55279000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:55274200-55279200	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr2:55274200-55279600	Active TSS	HMEC	breast
40	chr2:55274400-55275400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr2:55274400-55275800	Weak transcription	Small Intestine	intestine
42	chr2:55274400-55276000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:55274400-55278800	Active TSS	Fetal Brain Male	brain
44	chr2:55274600-55275200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:55274600-55275200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr2:55274600-55275200	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr2:55274600-55275200	Weak transcription	Pancreas	Pancrea
48	chr2:55274600-55275400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:55274600-55275400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:55274600-55275400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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