Variant report

Variant	rs59249742
Chromosome Location	chr3:135970177-135970178
allele	A/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	EBF1	chr3:135969854-135970676	GM12878	blood:	n/a	chr3:135970468-135970479 chr3:135970470-135970479
2	MXI1	chr3:135968554-135970729	SK-N-SH	brain:	n/a	n/a
3	RCOR1	chr3:135968845-135970213	K562	blood:	n/a	n/a
4	MAX	chr3:135968901-135970258	SK-N-SH	brain:	n/a	chr3:135969975-135969985
5	POLR2A	chr3:135968640-135970593	GM12878	blood:	n/a	n/a
6	MYC	chr3:135968702-135970404	K562	blood:	n/a	chr3:135969975-135969985
7	MAX	chr3:135969029-135970302	K562	blood:	n/a	chr3:135969975-135969985
8	CHD2	chr3:135968895-135970290	GM12878	blood:	n/a	n/a
9	HCFC1	chr3:135968899-135970307	K562	blood:	n/a	n/a
10	CTCF	chr3:135969974-135970185	LNCaP	prostate:	n/a	n/a
11	TBL1XR1	chr3:135968897-135970450	K562	blood:	n/a	n/a
12	POLR2A	chr3:135968842-135970657	K562	blood:	n/a	n/a
13	RUNX3	chr3:135968822-135970578	GM12878	blood:	n/a	n/a
14	CTCF	chr3:135969960-135970181	GM19239	blood:	n/a	n/a
15	POLR2A	chr3:135968899-135970272	K562	blood:	n/a	n/a
16	SPI1	chr3:135970071-135970449	GM12891	blood:	n/a	n/a
17	HCFC1	chr3:135968361-135970554	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:135968497-135970273	Raji	blood:	n/a	n/a
19	CTCF	chr3:135969924-135970182	GM12892	blood:	n/a	n/a
20	TCF7L2	chr3:135968902-135970203	Hela-S3	cervix:	n/a	n/a
21	MTA3	chr3:135969517-135970493	GM12878	blood:	n/a	n/a
22	ARID3A	chr3:135969875-135970236	K562	blood:	n/a	n/a
23	POLR2A	chr3:135968891-135970376	GM12878	blood:	n/a	n/a
24	CTCF	chr3:135969821-135970187	K562	blood:	n/a	n/a
25	EP300	chr3:135969764-135970494	K562	blood:	n/a	n/a
26	POLR2A	chr3:135968798-135970334	H1-hESC	embryonic stem cell:	n/a	n/a
27	IRF1	chr3:135968907-135970407	K562	blood:	n/a	chr3:135970232-135970242 chr3:135970231-135970243 chr3:135969422-135969436 chr3:135970230-135970244 chr3:135968941-135968950 chr3:135970231-135970248
28	CTCF	chr3:135969942-135970180	GM12891	blood:	n/a	n/a
29	MYC	chr3:135969085-135970591	MCF10A-Er-Src	breast:	n/a	chr3:135969975-135969985
30	BHLHE40	chr3:135968891-135970408	K562	blood:	n/a	chr3:135969109-135969125
31	NRF1	chr3:135969824-135970191	K562	blood:	n/a	n/a
32	YY1	chr3:135969751-135970237	HepG2	liver:	n/a	n/a
33	E2F6	chr3:135969728-135970201	H1-hESC	embryonic stem cell:	n/a	n/a
34	MYC	chr3:135968985-135970356	K562	blood:	n/a	chr3:135969975-135969985
35	GATA2	chr3:135969075-135970297	SH-SY5Y	brain:	n/a	n/a
36	MAX	chr3:135968881-135970303	A549	lung:	n/a	chr3:135969975-135969985
37	CTCF	chr3:135969938-135970190	GM19238	blood:	n/a	n/a
38	CTCF	chr3:135970040-135970190	GM12864	blood:	n/a	n/a
39	MYC	chr3:135968991-135970249	HepG2	liver:	n/a	chr3:135969975-135969985
40	NR2F2	chr3:135969502-135970374	K562	blood:	n/a	n/a
41	IRF1	chr3:135969011-135970205	K562	blood:	n/a	chr3:135969422-135969436
42	MAX	chr3:135968912-135970291	K562	blood:	n/a	chr3:135969975-135969985
43	BCLAF1	chr3:135969731-135970321	GM12878	blood:	n/a	chr3:135970232-135970241
44	CTCF	chr3:135970060-135970210	HRPEpiC	eye:	n/a	n/a
45	MAX	chr3:135968940-135970353	K562	blood:	n/a	chr3:135969975-135969985
46	POLR2A	chr3:135969879-135970276	K562	blood:	n/a	n/a
47	CEBPD	chr3:135969823-135970332	K562	blood:	n/a	n/a
48	MAZ	chr3:135968862-135970231	K562	blood:	n/a	n/a
49	POLR2A	chr3:135968573-135970337	GM15510	blood:	n/a	n/a
50	POLR2A	chr3:135968757-135970751	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:135968568..135972532-chr3:135974380..135977728,5	K562	blood:
2	chr3:135967895..135971293-chr3:135973278..135977937,5	MCF-7	breast:
3	chr3:135912206..135917353-chr3:135967047..135972220,20	MCF-7	breast:
4	chr3:135968756..135970580-chr3:136469634..136471998,2	K562	blood:
5	chr3:135969104..135971090-chr3:136470031..136473091,3	MCF-7	breast:
6	chr3:135912523..135919453-chr3:135966949..135972062,29	K562	blood:
7	chr3:135912324..135920790-chr3:135965276..135971841,24	K562	blood:
8	chr3:135913275..135917052-chr3:135966241..135970685,15	MCF-7	breast:
9	chr3:135967505..135970256-chr3:136469769..136472442,3	K562	blood:

Variant related genes	Relation type
PCCB	TF binding region
ENSG00000114054	Chromatin interaction
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs57648801	1.00[AFR][1000 genomes]
rs57657007	1.00[AFR][1000 genomes]
rs60479824	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv933522	chr3:135968919-135981180	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
4	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135968600-135970200	Active TSS	Fetal Lung	lung
2	chr3:135968600-135970200	Active TSS	Rectal Smooth Muscle	rectum
3	chr3:135968600-135970400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
4	chr3:135968600-135970400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:135968800-135970200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:135968800-135970200	Active TSS	A549	lung
7	chr3:135968800-135970400	Active TSS	Aorta	Aorta
8	chr3:135968800-135970600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:135969000-135970200	Active TSS	Brain Angular Gyrus	brain
10	chr3:135969400-135970200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr3:135969400-135970200	Flanking Active TSS	Liver	Liver
12	chr3:135969400-135970400	Flanking Active TSS	HUVEC	blood vessel
13	chr3:135969600-135970200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr3:135969600-135970200	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr3:135969600-135970200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr3:135969600-135970200	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr3:135969600-135970200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:135969600-135970200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr3:135969600-135970200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr3:135969600-135970200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr3:135969600-135970200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:135969600-135970200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr3:135969600-135970200	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr3:135969600-135970200	Flanking Active TSS	Stomach Mucosa	stomach
25	chr3:135969600-135970400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:135969600-135970400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr3:135969600-135970400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:135969600-135970400	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr3:135969600-135970400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr3:135969600-135970400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr3:135969600-135970400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:135969600-135970400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr3:135969600-135970400	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr3:135969600-135970400	Flanking Active TSS	Fetal Heart	heart
35	chr3:135969600-135970400	Flanking Active TSS	HSMMtube	muscle
36	chr3:135969600-135970400	Flanking Active TSS	NH-A	brain
37	chr3:135969600-135970600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr3:135969600-135970600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:135969600-135970600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:135969600-135970600	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr3:135969600-135970600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr3:135969600-135970600	Flanking Active TSS	HMEC	breast
43	chr3:135969600-135970600	Flanking Active TSS	NHLF	lung
44	chr3:135969600-135970600	Flanking Active TSS	Osteobl	bone
45	chr3:135969600-135970800	Flanking Active TSS	GM12878-XiMat	blood
46	chr3:135969600-135970800	Flanking Active TSS	HepG2	liver
47	chr3:135969800-135970200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:135969800-135970200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
49	chr3:135969800-135970200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:135969800-135970200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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