Variant report

Variant	rs6544225
Chromosome Location	chr2:39621264-39621265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39619324..39621910-chr2:39662875..39665257,2	K562	blood:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10490305	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11886110	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11886434	0.84[AFR][1000 genomes]
rs11895366	0.92[AFR][1000 genomes]
rs11898704	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11902188	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17023620	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17038958	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55750780	0.81[AFR][1000 genomes]
rs55961227	0.97[AFR][1000 genomes]
rs56850142	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56928728	0.93[AFR][1000 genomes]
rs57084694	0.82[AFR][1000 genomes]
rs58005382	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58824151	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59459399	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59896787	0.82[AFR][1000 genomes]
rs60394429	0.92[AFR][1000 genomes]
rs61219633	0.90[AFR][1000 genomes]
rs6712399	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6718000	0.84[ASN][1000 genomes]
rs6723987	0.89[AFR][1000 genomes]
rs6725784	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6727395	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6751506	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73923844	0.81[AFR][1000 genomes]
rs73923848	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73923887	0.97[AFR][1000 genomes]
rs73923888	0.97[AFR][1000 genomes]
rs73923889	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73923895	0.95[AFR][1000 genomes]
rs73924011	0.84[AFR][1000 genomes]
rs73924013	0.84[AFR][1000 genomes]
rs73924016	0.82[AFR][1000 genomes]
rs7565210	0.89[AFR][1000 genomes]
rs7591563	0.97[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7599017	0.98[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic 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	21 gene(s)	inside rSNPs	diseases
3	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
4	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
6	chr2:39607000-39626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:39607400-39624800	Weak transcription	Stomach Mucosa	stomach
8	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:39608000-39622800	Weak transcription	Fetal Kidney	kidney
10	chr2:39608400-39626200	Weak transcription	Brain Substantia Nigra	brain
11	chr2:39609200-39621600	Weak transcription	Lung	lung
12	chr2:39609400-39621600	Weak transcription	HSMM	muscle
13	chr2:39609600-39621400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:39609600-39621600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:39609600-39621600	Weak transcription	NH-A	brain
16	chr2:39609600-39621600	Weak transcription	Osteobl	bone
17	chr2:39609600-39626400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:39610200-39621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:39610200-39626400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:39613000-39621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:39613600-39621600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:39613600-39621600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:39613800-39630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:39614000-39628000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:39614800-39621600	Weak transcription	Pancreas	Pancrea
26	chr2:39615600-39621400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:39615800-39626800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:39616000-39622200	Weak transcription	Fetal Stomach	stomach
29	chr2:39616000-39626400	Weak transcription	Gastric	stomach
30	chr2:39617600-39626200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:39617600-39626400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:39617800-39621400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:39617800-39621400	Weak transcription	NHDF-Ad	bronchial
34	chr2:39617800-39621600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:39617800-39621600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:39617800-39621600	Weak transcription	Ovary	ovary
37	chr2:39617800-39626200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:39617800-39628200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:39617800-39628400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:39617800-39630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:39618000-39633400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:39618200-39623200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:39619000-39621800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:39619200-39629600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:39619400-39621400	Weak transcription	Right Atrium	heart
46	chr2:39619400-39622400	Weak transcription	Fetal Brain Male	brain
47	chr2:39619800-39625600	Enhancers	HepG2	liver
48	chr2:39620000-39629400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:39620200-39635600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr2:39620400-39622000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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