Variant report

Variant	rs2968782
Chromosome Location	chr2:55342116-55342117
allele	G/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	chr2:55341662-55344054	K562	blood:	n/a	chr2:55343402-55343414 chr2:55343403-55343412 chr2:55342694-55342710

No.	Distal block	Cell Line	Cell type
1	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
2	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
3	chr2:55339781..55342552-chr2:55346442..55349594,4	K562	blood:
4	chr2:55341952..55344762-chr2:55357897..55359885,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2920847	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920850	0.93[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2920851	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2920864	0.85[ASN][1000 genomes]
rs2920865	0.85[ASN][1000 genomes]
rs2920866	0.85[ASN][1000 genomes]
rs2920867	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2920868	0.92[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2968780	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2968800	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2968801	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2968802	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2972062	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972093	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972095	0.84[AMR][1000 genomes]
rs34307608	0.83[ASN][1000 genomes]
rs4672024	0.81[JPT][hapmap]

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	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55329600-55342600	Weak transcription	NHEK	skin
2	chr2:55332000-55343400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:55337400-55342800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:55337400-55342800	Weak transcription	HMEC	breast
6	chr2:55338400-55343400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:55338400-55343400	Enhancers	Primary hematopoietic stem cells	blood
8	chr2:55338600-55343800	Enhancers	Fetal Muscle Leg	muscle
9	chr2:55339200-55343000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:55339400-55351000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:55339600-55342200	Weak transcription	Hela-S3	cervix
12	chr2:55339600-55342600	Enhancers	A549	lung
13	chr2:55339600-55345800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:55339600-55345800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:55339600-55345800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:55339600-55346800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:55339600-55347000	Weak transcription	Left Ventricle	heart
18	chr2:55339800-55342600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:55339800-55343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:55339800-55343000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:55339800-55344400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:55339800-55345600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:55339800-55345800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:55339800-55347000	Weak transcription	Lung	lung
25	chr2:55340000-55342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:55340000-55343600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:55340000-55343600	Enhancers	NHLF	lung
28	chr2:55340000-55345600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:55340200-55342400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:55340200-55342600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:55340200-55343200	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr2:55340200-55346200	Weak transcription	Fetal Brain Female	brain
33	chr2:55340400-55342600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:55340400-55343000	Weak transcription	Small Intestine	intestine
35	chr2:55340400-55344200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:55340400-55345800	Enhancers	K562	blood
37	chr2:55340600-55342600	Weak transcription	HUVEC	blood vessel
38	chr2:55340600-55344400	Weak transcription	Brain Germinal Matrix	brain
39	chr2:55340600-55345200	Weak transcription	Fetal Brain Male	brain
40	chr2:55340600-55347000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:55340800-55342200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:55340800-55342400	Weak transcription	Fetal Heart	heart
43	chr2:55340800-55342800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:55340800-55342800	Weak transcription	Right Atrium	heart
45	chr2:55340800-55343200	Enhancers	Brain Cingulate Gyrus	brain
46	chr2:55340800-55343800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:55340800-55344600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:55340800-55345600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr2:55340800-55346000	Weak transcription	Spleen	Spleen
50	chr2:55340800-55347200	Weak transcription	Rectal Mucosa Donor 29	rectum

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