Variant report

Variant	rs12499989
Chromosome Location	chr4:77068382-77068383
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	GATA1	chr4:77068148-77070055	PBDE	blood:	n/a	chr4:77068507-77068514 chr4:77068392-77068401 chr4:77068860-77068867 chr4:77068507-77068517 chr4:77068500-77068521 chr4:77068860-77068870 chr4:77068505-77068514 chr4:77068855-77068871
2	MXI1	chr4:77068304-77070491	IMR90	lung:	n/a	n/a
3	TBL1XR1	chr4:77068302-77068452	K562	blood:	n/a	n/a
4	POLR2A	chr4:77068325-77074118	K562	blood:	n/a	n/a
5	JUN	chr4:77068215-77070443	K562	blood:	n/a	chr4:77068511-77068520 chr4:77068323-77068331
6	MXI1	chr4:77068209-77070656	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:77050141..77053778-chr4:77066166..77070004,4	MCF-7	breast:
2	chr4:77027487..77029799-chr4:77068169..77070683,2	K562	blood:
3	chr4:77066331..77070645-chr4:77133023..77136401,5	K562	blood:
4	chr4:76860116..76861672-chr4:77068138..77069757,2	MCF-7	breast:
5	chr4:77065569..77067596-chr4:77067716..77071190,4	MCF-7	breast:
6	chr4:77067778..77069460-chr4:77134577..77136401,2	K562	blood:
7	chr4:77054225..77056351-chr4:77067941..77069735,2	MCF-7	breast:
8	chr4:77068043..77069924-chr4:77085351..77088646,3	K562	blood:

Variant related genes	Relation type
NUP54	TF binding region
ENSG00000138760	Chromatin interaction
ENSG00000189157	Chromatin interaction
ENSG00000138744	Chromatin interaction
ENSG00000156219	Chromatin interaction
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11097233	0.85[EUR][1000 genomes]
rs17001561	0.80[ASN][1000 genomes]
rs2119733	0.80[ASN][1000 genomes]
rs56102101	0.87[ASN][1000 genomes]
rs61750814	1.00[ASN][1000 genomes]
rs6829784	0.80[ASN][1000 genomes]
rs6835324	0.80[ASN][1000 genomes]
rs72655532	0.80[ASN][1000 genomes]
rs72655539	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv470047	chr4:77033590-77096777	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1008318	chr4:77042356-77095658	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv537144	chr4:77042356-77095658	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1000539	chr4:77042356-77105492	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv1000178	chr4:77053046-77113080	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 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	chr4:77028000-77068600	Weak transcription	Gastric	stomach
2	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
3	chr4:77035000-77068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:77035200-77068600	Weak transcription	Pancreas	Pancrea
5	chr4:77035600-77068400	Weak transcription	Right Ventricle	heart
6	chr4:77039000-77068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:77045000-77068600	Weak transcription	Spleen	Spleen
8	chr4:77051400-77068600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:77058800-77068400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:77062400-77068600	Weak transcription	Aorta	Aorta
11	chr4:77062400-77068600	Weak transcription	Esophagus	oesophagus
12	chr4:77062400-77068600	Weak transcription	Lung	lung
13	chr4:77062600-77068400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:77062600-77068600	Weak transcription	Left Ventricle	heart
15	chr4:77065200-77068600	Weak transcription	Placenta	Placenta
16	chr4:77065400-77068400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:77065600-77068400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:77065600-77068400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:77065600-77068400	Weak transcription	HSMMtube	muscle
20	chr4:77066000-77068400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr4:77066000-77070800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr4:77066600-77068400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:77066600-77068400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr4:77066600-77070800	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr4:77066800-77068400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr4:77066800-77068400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr4:77067000-77068400	Enhancers	Brain Cingulate Gyrus	brain
28	chr4:77067000-77069000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:77067000-77070600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr4:77067200-77068400	Enhancers	Primary B cells from cord blood	blood
31	chr4:77067200-77068600	Enhancers	Stomach Mucosa	stomach
32	chr4:77067200-77070600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:77067200-77070600	Active TSS	K562	blood
34	chr4:77067200-77070800	Active TSS	H1 Cell Line	embryonic stem cell
35	chr4:77067400-77068400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:77067400-77068400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:77067400-77068400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:77067400-77068400	Enhancers	Brain Angular Gyrus	brain
39	chr4:77067400-77068400	Flanking Active TSS	GM12878-XiMat	blood
40	chr4:77067400-77068600	Flanking Active TSS	Dnd41	blood
41	chr4:77067400-77068600	Flanking Active TSS	NHEK	skin
42	chr4:77067400-77068800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:77067400-77068800	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr4:77067400-77069000	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr4:77067400-77070800	Active TSS	A549	lung
46	chr4:77067400-77071200	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr4:77067600-77068400	Enhancers	Brain Anterior Caudate	brain
48	chr4:77067600-77068400	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr4:77067600-77068400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr4:77067600-77068400	Enhancers	Brain Substantia Nigra	brain

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