Variant report

Variant	rs13004436
Chromosome Location	chr2:55836056-55836057
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55452223..55454388-chr2:55835681..55838374,2	K562	blood:
2	chr2:55820891..55824510-chr2:55834569..55837738,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1013138	0.85[CHB][hapmap]
rs12618859	0.83[CHB][hapmap]
rs12623293	0.83[AMR][1000 genomes]
rs12623937	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12987272	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12993839	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12994656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12998664	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes]
rs12998780	0.84[CHB][hapmap]
rs12999966	0.81[CHB][hapmap]
rs13001452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13007719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13009649	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13010217	0.84[CHB][hapmap]
rs13014123	0.82[ASN][1000 genomes]
rs13015243	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13015744	0.90[CHB][hapmap]
rs13019595	0.81[AMR][1000 genomes]
rs13025331	0.84[CHB][hapmap]
rs13025994	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13030396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1542643	0.80[AMR][1000 genomes]
rs17737233	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[AMR][1000 genomes]
rs1867334	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2054729	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291336	0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs34400247	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35057183	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35124901	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35255044	0.91[AMR][1000 genomes]
rs35861320	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35968359	0.90[AMR][1000 genomes]
rs3748944	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3748952	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3791654	0.83[CHB][hapmap]
rs3828238	0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs6753530	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes]
rs878124	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 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	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
3	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
4	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:55803000-55838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:55824400-55837400	Weak transcription	Fetal Kidney	kidney
7	chr2:55826000-55839200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:55826000-55841600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:55826200-55842600	Weak transcription	Right Ventricle	heart
10	chr2:55826200-55843000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:55828200-55843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:55828400-55838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:55829800-55838400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:55829800-55838400	Weak transcription	HMEC	breast
15	chr2:55829800-55838800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:55829800-55842800	Weak transcription	Colonic Mucosa	Colon
17	chr2:55830000-55838000	Weak transcription	Brain Germinal Matrix	brain
18	chr2:55830000-55838200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:55830000-55838600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:55830200-55837600	Weak transcription	NHEK	skin
21	chr2:55830200-55838000	Weak transcription	Adipose Nuclei	Adipose
22	chr2:55830200-55838200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:55830400-55836400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:55830400-55837400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:55830400-55837400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:55830400-55837400	Weak transcription	Fetal Lung	lung
27	chr2:55830400-55837400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:55830400-55837600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:55830400-55838000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:55830400-55838000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:55830400-55838000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:55830400-55838000	Weak transcription	Esophagus	oesophagus
33	chr2:55830400-55838000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:55830400-55838200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:55830400-55838200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:55830400-55838200	Weak transcription	Thymus	Thymus
37	chr2:55830400-55838400	Weak transcription	Brain Anterior Caudate	brain
38	chr2:55830400-55838400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:55830400-55838600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:55830400-55838800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:55830400-55838800	Weak transcription	Spleen	Spleen
42	chr2:55830400-55841000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:55830400-55842800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:55830400-55843600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:55830400-55843600	Weak transcription	Aorta	Aorta
46	chr2:55830600-55837600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:55830600-55838000	Weak transcription	HUVEC	blood vessel
48	chr2:55830600-55838200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:55830600-55838400	Weak transcription	Dnd41	blood
50	chr2:55830600-55838800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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