Variant report

Variant	rs10031491
Chromosome Location	chr4:54424437-54424438
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	GATA2	chr4:54424287-54425344	HUVEC	blood vessel:	n/a	chr4:54424889-54424898 chr4:54425266-54425274
2	CTCF	chr4:54424360-54424510	WERI-Rb-1	eye:	n/a	n/a
3	CTCF	chr4:54424356-54424508	Medullo	brain:	n/a	n/a
4	POLR2A	chr4:54424217-54425194	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr4:54424156-54425082	HUVEC	blood vessel:	n/a	n/a
6	JUN	chr4:54424386-54425083	HUVEC	blood vessel:	n/a	chr4:54424887-54424897 chr4:54424887-54424897 chr4:54424888-54424897 chr4:54424887-54424897 chr4:54424887-54424897
7	CTCF	chr4:54424320-54424470	HCM	heart:	n/a	n/a
8	PBX3	chr4:54424361-54425474	SK-N-SH	brain:	n/a	n/a
9	JUND	chr4:54424076-54425890	SK-N-SH	brain:	n/a	chr4:54424887-54424897 chr4:54424887-54424897 chr4:54424888-54424897 chr4:54424887-54424897 chr4:54424886-54424897 chr4:54424887-54424897
10	CTCF	chr4:54424420-54424570	AG10803	skin:	n/a	n/a
11	CTCF	chr4:54424340-54424490	HBMEC	blood vessel:	n/a	n/a
12	RAD21	chr4:54424186-54424513	SK-N-SH_RA	brain:	n/a	n/a
13	REST	chr4:54424067-54425193	H1-neurons	neurons:	n/a	chr4:54424625-54424638 chr4:54424621-54424641
14	FOS	chr4:54424404-54425744	HUVEC	blood vessel:	n/a	chr4:54424887-54424897 chr4:54424887-54424897 chr4:54424886-54424897 chr4:54424888-54424897 chr4:54424887-54424897 chr4:54424887-54424897
15	CTCF	chr4:54424394-54424455	ProgFib	skin:	n/a	n/a
16	PBX3	chr4:54424400-54425784	SK-N-SH	brain:	n/a	n/a
17	CTCF	chr4:54424400-54424550	HUVEC	blood vessel:	n/a	n/a
18	RAD21	chr4:54424296-54424604	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr4:54424340-54424490	AG10803	skin:	n/a	n/a
20	CTCF	chr4:54424340-54424490	AG04449	skin:	n/a	n/a
21	CTCF	chr4:54424338-54424499	Fibrobl	skin:	n/a	n/a
22	POLR2A	chr4:54423962-54425055	U87	brain:	n/a	n/a
23	CTCF	chr4:54424371-54424499	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr4:54424088-54425133	H1-neurons	neurons:	n/a	n/a
25	TBP	chr4:54424337-54424537	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr4:54424115-54424558	U87	brain:	n/a	n/a
27	POLR2A	chr4:54424048-54425055	U87	brain:	n/a	n/a
28	CTCF	chr4:54424360-54424510	SK-N-SH_RA	brain:	n/a	n/a
29	RAD21	chr4:54424129-54424664	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr4:54424360-54424510	HRPEpiC	eye:	n/a	n/a
31	REST	chr4:54423856-54425428	H1-neurons	neurons:	n/a	chr4:54424625-54424638 chr4:54424621-54424641
32	CTCF	chr4:54424300-54424450	HA-sp	spinal cord:	n/a	n/a
33	CTCF	chr4:54424350-54424494	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr4:54424357-54424506	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54422826..54425638-chr4:54441599..54444250,2	MCF-7	breast:

Variant related genes	Relation type
LNX1	TF binding region
ENSG00000173966	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10000457	0.82[MKK][hapmap]
rs10007397	0.88[AFR][1000 genomes]
rs12507175	1.00[CHB][hapmap]
rs17083038	0.96[AFR][1000 genomes]
rs57991612	0.96[AFR][1000 genomes]
rs9654328	0.91[AFR][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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54390400-54430400	Weak transcription	Stomach Mucosa	stomach
2	chr4:54409200-54427000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:54412200-54442400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:54413800-54426000	Weak transcription	Right Ventricle	heart
5	chr4:54416000-54438000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:54419200-54424600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr4:54419800-54430400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:54420000-54424600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:54420000-54424800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:54420000-54437600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:54421000-54424800	Active TSS	Fetal Brain Female	brain
12	chr4:54421000-54424800	Enhancers	Fetal Heart	heart
13	chr4:54421400-54424600	Weak transcription	Hela-S3	cervix
14	chr4:54421400-54428400	Weak transcription	Fetal Stomach	stomach
15	chr4:54421400-54437600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:54421600-54437000	Weak transcription	Pancreas	Pancrea
17	chr4:54422400-54424600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:54423400-54425200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:54423600-54424600	Active TSS	Aorta	Aorta
20	chr4:54423600-54425000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr4:54423800-54424600	Enhancers	NHEK	skin
22	chr4:54423800-54424800	Enhancers	Left Ventricle	heart
23	chr4:54423800-54424800	Flanking Active TSS	HSMM	muscle
24	chr4:54423800-54425200	Enhancers	Placenta	Placenta
25	chr4:54423800-54425400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:54423800-54425400	Enhancers	Fetal Muscle Leg	muscle
27	chr4:54423800-54426000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:54423800-54426000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:54423800-54426000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:54424000-54424600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:54424000-54424600	Enhancers	Fetal Muscle Trunk	muscle
32	chr4:54424000-54424800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:54424000-54424800	Enhancers	Primary hematopoietic stem cells	blood
34	chr4:54424000-54425000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:54424000-54425000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:54424000-54425000	Flanking Active TSS	HSMMtube	muscle
37	chr4:54424000-54425000	Flanking Active TSS	NHDF-Ad	bronchial
38	chr4:54424000-54425200	Enhancers	Adipose Nuclei	Adipose
39	chr4:54424000-54425200	Enhancers	Esophagus	oesophagus
40	chr4:54424000-54425200	Strong transcription	Fetal Intestine Small	intestine
41	chr4:54424000-54425200	Enhancers	Lung	lung
42	chr4:54424000-54425200	Enhancers	Spleen	Spleen
43	chr4:54424000-54425400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:54424000-54425400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr4:54424000-54425400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:54424000-54425400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr4:54424000-54425400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:54424000-54425400	Strong transcription	Liver	Liver
49	chr4:54424000-54425400	Flanking Active TSS	HUVEC	blood vessel
50	chr4:54424000-54425800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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