Variant report

Variant	rs369942694
Chromosome Location	chr4:48343318-48343319
allele	C/T
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	JUN	chr4:48342560-48343706	K562	blood:	n/a	chr4:48342747-48342758 chr4:48342726-48342735 chr4:48343389-48343398 chr4:48343239-48343248
2	YY1	chr4:48343015-48344553	SK-N-SH	brain:	n/a	chr4:48343494-48343516 chr4:48343239-48343250 chr4:48343506-48343516 chr4:48343512-48343523 chr4:48343499-48343518 chr4:48343507-48343515
3	POLR2A	chr4:48342963-48344353	GM12878	blood:	n/a	n/a
4	SP1	chr4:48342819-48343845	HCT-116	colon:	n/a	chr4:48343387-48343396 chr4:48343341-48343350 chr4:48343361-48343370 chr4:48343176-48343186 chr4:48343340-48343352 chr4:48343360-48343372 chr4:48343387-48343401 chr4:48343360-48343372 chr4:48343388-48343397 chr4:48343236-48343248 chr4:48343361-48343370 chr4:48343176-48343186 chr4:48343362-48343371 chr4:48343386-48343398 chr4:48343342-48343351 chr4:48343237-48343246 chr4:48343236-48343248 chr4:48343361-48343371 chr4:48343386-48343398 chr4:48343341-48343350 chr4:48343387-48343396
5	TBP	chr4:48342977-48343735	HepG2	liver:	n/a	n/a
6	SIN3A	chr4:48342884-48344017	GM12878	blood:	n/a	chr4:48343390-48343401 chr4:48343422-48343431 chr4:48343093-48343104
7	ELF1	chr4:48342912-48343945	K562	blood:	n/a	chr4:48343238-48343250
8	TBP	chr4:48343011-48344491	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr4:48342918-48344085	GM12891	blood:	n/a	n/a
10	POLR2A	chr4:48342997-48344741	H1-neurons	neurons:	n/a	n/a
11	PAX5	chr4:48342961-48344122	GM12892	blood:	n/a	chr4:48343359-48343378
12	YY1	chr4:48342984-48344136	GM12891	blood:	n/a	chr4:48343494-48343516 chr4:48343239-48343250 chr4:48343506-48343516 chr4:48343512-48343523 chr4:48343499-48343518 chr4:48343507-48343515
13	POLR2A	chr4:48342228-48344387	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr4:48342702-48344406	HUVEC	blood vessel:	n/a	n/a
15	MYC	chr4:48343104-48343334	MCF-7	breast:	n/a	n/a
16	ELF1	chr4:48342954-48343332	HepG2	liver:	n/a	chr4:48343238-48343250
17	BHLHE40	chr4:48342757-48343684	GM12878	blood:	n/a	chr4:48343422-48343438 chr4:48343391-48343407 chr4:48343576-48343592 chr4:48343424-48343440
18	GABPA	chr4:48343039-48343636	HepG2	liver:	n/a	chr4:48343238-48343247 chr4:48343552-48343566
19	YY1	chr4:48343061-48343326	H1-hESC	embryonic stem cell:	n/a	chr4:48343239-48343250
20	POLR2A	chr4:48342953-48343323	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr4:48343220-48343370	GM12869	blood:	n/a	chr4:48343251-48343264
22	RFX5	chr4:48342863-48343750	Hela-S3	cervix:	n/a	n/a
23	E2F4	chr4:48342908-48343712	MCF10A-Er-Src	breast:	n/a	chr4:48343404-48343414 chr4:48343238-48343247
24	PML	chr4:48342508-48344642	GM12878	blood:	n/a	n/a
25	YY1	chr4:48343311-48343770	A549	lung:	n/a	chr4:48343494-48343516 chr4:48343506-48343516 chr4:48343512-48343523 chr4:48343499-48343518 chr4:48343507-48343515
26	POLR2A	chr4:48342886-48343364	GM12891	blood:	n/a	n/a
27	POLR2A	chr4:48342903-48343803	HCT-116	colon:	n/a	n/a
28	SMARCB1	chr4:48342964-48344702	Hela-S3	cervix:	n/a	n/a
29	YY1	chr4:48342952-48343755	SK-N-SH_RA	brain:	n/a	chr4:48343494-48343516 chr4:48343239-48343250 chr4:48343506-48343516 chr4:48343512-48343523 chr4:48343499-48343518 chr4:48343507-48343515
30	POLR2A	chr4:48342462-48343728	K562	blood:	n/a	n/a
31	UBTF	chr4:48342320-48345277	K562	blood:	n/a	n/a
32	TAF1	chr4:48342948-48343820	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr4:48342893-48344029	GM12878	blood:	n/a	n/a
34	MXI1	chr4:48342952-48344664	HepG2	liver:	n/a	n/a
35	YY1	chr4:48343309-48343775	GM12891	blood:	n/a	chr4:48343494-48343516 chr4:48343506-48343516 chr4:48343512-48343523 chr4:48343499-48343518 chr4:48343507-48343515
36	POLR2A	chr4:48342555-48344209	MCF10A-Er-Src	breast:	n/a	n/a
37	NR2F2	chr4:48342426-48343797	K562	blood:	n/a	n/a
38	SP1	chr4:48342968-48343702	GM12878	blood:	n/a	chr4:48343387-48343396 chr4:48343341-48343350 chr4:48343361-48343370 chr4:48343176-48343186 chr4:48343340-48343352 chr4:48343360-48343372 chr4:48343387-48343401 chr4:48343360-48343372 chr4:48343388-48343397 chr4:48343236-48343248 chr4:48343361-48343370 chr4:48343176-48343186 chr4:48343362-48343371 chr4:48343386-48343398 chr4:48343342-48343351 chr4:48343237-48343246 chr4:48343236-48343248 chr4:48343361-48343371 chr4:48343386-48343398 chr4:48343341-48343350 chr4:48343387-48343396
39	POLR2A	chr4:48342315-48344444	IMR90	lung:	n/a	n/a
40	SIN3A	chr4:48342275-48344914	H1-hESC	embryonic stem cell:	n/a	chr4:48344167-48344178 chr4:48343390-48343401 chr4:48343422-48343431 chr4:48344167-48344180 chr4:48343093-48343104
41	HDAC2	chr4:48342953-48343344	MCF-7	breast:	n/a	n/a
42	ELK1	chr4:48342885-48343608	Hela-S3	cervix:	n/a	n/a
43	TAF1	chr4:48342954-48343831	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr4:48342498-48344353	PFSK-1	brain:	n/a	n/a
45	CEBPD	chr4:48342938-48343358	K562	blood:	n/a	n/a
46	EGR1	chr4:48343017-48343417	ECC-1	luminal epithelium:	n/a	chr4:48343178-48343191 chr4:48343179-48343189 chr4:48343238-48343248 chr4:48343177-48343191
47	RUNX3	chr4:48342646-48343804	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:48342366-48344589	K562	blood:	n/a	n/a
49	TAF1	chr4:48342843-48344341	ECC-1	luminal epithelium:	n/a	n/a
50	GABPA	chr4:48342745-48343771	HL-60	blood:	n/a	chr4:48343238-48343247 chr4:48343552-48343566

No.	Distal block	Cell Line	Cell type
1	chr17:79479311..79479820-chr4:48342792..48343547,2	Hela-S3	cervix:
2	chr4:48341542..48343650-chr4:48378558..48381453,2	K562	blood:
3	chr4:48270141..48273598-chr4:48341900..48344865,7	K562	blood:
4	chr4:48341515..48344236-chr4:48506268..48509029,2	K562	blood:
5	chr2:96873883..96874519-chr4:48342610..48343559,2	NB4	blood:
6	chr4:48270358..48273390-chr4:48340605..48344777,4	MCF-7	breast:
7	chr3:42641898..42642685-chr4:48342789..48343555,2	Hela-S3	cervix:
8	chr4:48269261..48273807-chr4:48342628..48344865,6	K562	blood:
9	chr4:48341909..48343469-chr4:48483589..48486077,2	K562	blood:

Variant related genes	Relation type
SLAIN2	TF binding region
ENSG00000093183	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000075539	Chromatin interaction
ENSG00000145248	Chromatin interaction
ENSG00000109171	Chromatin interaction
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv3377721	chr4:48342220-48345068	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48342000-48345400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:48342000-48345400	Active TSS	Fetal Intestine Large	intestine
3	chr4:48342000-48345600	Active TSS	Fetal Intestine Small	intestine
4	chr4:48342200-48343600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:48342200-48344200	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr4:48342200-48344400	Active TSS	Colonic Mucosa	Colon
7	chr4:48342200-48344600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr4:48342200-48345200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr4:48342200-48345200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:48342200-48345200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr4:48342200-48345200	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr4:48342200-48345400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:48342200-48345400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:48342200-48345400	Active TSS	Brain Anterior Caudate	brain
15	chr4:48342200-48345600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr4:48342200-48345800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:48342400-48343400	Active TSS	Right Atrium	heart
18	chr4:48342400-48344400	Active TSS	Brain Cingulate Gyrus	brain
19	chr4:48342400-48344400	Active TSS	Brain Substantia Nigra	brain
20	chr4:48342400-48344800	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr4:48342400-48344800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:48342400-48344800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:48342400-48344800	Active TSS	Brain Hippocampus Middle	brain
24	chr4:48342400-48344800	Active TSS	Esophagus	oesophagus
25	chr4:48342400-48345000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:48342400-48345000	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr4:48342400-48345000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:48342400-48345000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr4:48342400-48345200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr4:48342400-48345200	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr4:48342400-48345200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:48342400-48345200	Active TSS	Brain Angular Gyrus	brain
33	chr4:48342400-48345200	Active TSS	Colon Smooth Muscle	Colon
34	chr4:48342400-48345200	Active TSS	Fetal Muscle Trunk	muscle
35	chr4:48342400-48345200	Active TSS	Left Ventricle	heart
36	chr4:48342400-48345400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:48342400-48345400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:48342400-48345400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr4:48342400-48345400	Active TSS	Ovary	ovary
40	chr4:48342400-48345600	Active TSS	Brain Germinal Matrix	brain
41	chr4:48342400-48346000	Active TSS	Aorta	Aorta
42	chr4:48342400-48346200	Active TSS	Psoas Muscle	Psoas
43	chr4:48342400-48346200	Active TSS	Stomach Smooth Muscle	stomach
44	chr4:48342400-48346600	Active TSS	Right Ventricle	heart
45	chr4:48342600-48343600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:48342600-48343800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:48342600-48343800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:48342600-48343800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:48342600-48343800	Active TSS	HepG2	liver
50	chr4:48342600-48344200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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