Variant report

Variant	rs2068135
Chromosome Location	chr4:130016221-130016222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr4:130012946-130016268	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr4:130015959-130016451	MCF10A-Er-Src	breast:	n/a	n/a
3	KAP1	chr4:130016192-130016743	K562	blood:	n/a	n/a
4	TBL1XR1	chr4:130015970-130017767	K562	blood:	n/a	n/a
5	ARID3A	chr4:130015591-130017978	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:130012621..130015537-chr4:130015842..130017627,2	K562	blood:
2	chr4:128703531..128705249-chr4:130014655..130017577,2	K562	blood:
3	chr4:129731090..129733904-chr4:130015000..130016574,3	K562	blood:
4	chr4:129730340..129733748-chr4:130013373..130016609,5	K562	blood:

No data

Variant related genes	Relation type
C4orf33	TF binding region
SCLT1	TF binding region
ENSG00000151466	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000151470	Chromatin interaction
ENSG00000164070	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10518543	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12648004	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12651152	0.84[EUR][1000 genomes]
rs13106626	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13111663	0.81[EUR][1000 genomes]
rs13124870	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13126896	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13127992	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13136209	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13138537	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13139306	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13151322	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs17014149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17014190	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17184802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2068136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28643269	0.83[ASN][1000 genomes]
rs33999735	0.90[ASN][1000 genomes]
rs34044129	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34302928	0.93[ASN][1000 genomes]
rs34483420	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs35002630	0.92[EUR][1000 genomes]
rs35053690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35128288	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35149191	0.90[ASN][1000 genomes]
rs35199409	0.93[ASN][1000 genomes]
rs35259423	0.85[AMR][1000 genomes]
rs35349408	0.96[EUR][1000 genomes]
rs35388412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35412182	0.83[ASN][1000 genomes]
rs36000518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36101862	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36124477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36128858	0.90[ASN][1000 genomes]
rs71612197	0.92[EUR][1000 genomes]
rs71612199	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71613905	0.90[ASN][1000 genomes]
rs71613907	0.90[ASN][1000 genomes]
rs71613908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71613914	0.84[EUR][1000 genomes]

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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130011200-130016400	Active TSS	GM12878-XiMat	blood
2	chr4:130012800-130018600	Active TSS	K562	blood
3	chr4:130014800-130017200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:130014800-130017200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:130015000-130017200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:130015000-130017200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:130015000-130017200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:130015000-130017200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:130015200-130017000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:130015200-130017000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:130015200-130017000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:130015200-130017200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:130015200-130017200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:130015200-130017200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:130015200-130017200	Weak transcription	Esophagus	oesophagus
16	chr4:130015200-130017200	Weak transcription	Placenta	Placenta
17	chr4:130015200-130017200	Weak transcription	Left Ventricle	heart
18	chr4:130015200-130017200	Weak transcription	Lung	lung
19	chr4:130015200-130017200	Weak transcription	Pancreas	Pancrea
20	chr4:130015200-130017200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:130015200-130017200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:130015200-130017200	Weak transcription	Small Intestine	intestine
23	chr4:130015200-130017200	Weak transcription	HSMM	muscle
24	chr4:130015200-130017200	Weak transcription	HSMMtube	muscle
25	chr4:130015400-130016400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:130015400-130016600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr4:130015400-130016800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr4:130015400-130016800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr4:130015400-130017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:130015400-130017000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:130015400-130017000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:130015400-130017000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:130015400-130017000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:130015400-130017000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:130015400-130017000	Enhancers	Primary T cells from cord blood	blood
36	chr4:130015400-130017000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:130015400-130017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:130015400-130017000	Weak transcription	Liver	Liver
39	chr4:130015400-130017000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:130015400-130017000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:130015400-130017000	Weak transcription	Colonic Mucosa	Colon
42	chr4:130015400-130017000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:130015400-130017000	Weak transcription	Fetal Intestine Large	intestine
44	chr4:130015400-130017000	Weak transcription	Fetal Thymus	thymus
45	chr4:130015400-130017000	Weak transcription	Ovary	ovary
46	chr4:130015400-130017000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr4:130015400-130017000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr4:130015400-130017000	Weak transcription	Right Atrium	heart
49	chr4:130015400-130017000	Weak transcription	Stomach Mucosa	stomach
50	chr4:130015400-130017000	Weak transcription	A549	lung

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