Variant report

Variant	rs1353644
Chromosome Location	chr2:47406164-47406165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:47382524-47406811	PFSK-1	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47399756..47406251-chr2:47447036..47455846,12	MCF-7	breast:
2	chr2:47399705..47406684-chr2:47448496..47456698,16	K562	blood:
3	chr2:47405558..47407711-chr2:47452457..47454896,2	K562	blood:
4	chr2:47405335..47406963-chr2:48008151..48011120,2	K562	blood:
5	chr2:47404373..47406414-chr2:47509583..47511440,2	MCF-7	breast:
6	chr2:47140743..47148534-chr2:47401019..47406419,10	MCF-7	breast:

No data

Variant related genes	Relation type
CALM2	TF binding region
ENSG00000273269	TF binding region
ENSG00000068724	Chromatin interaction
ENSG00000116062	Chromatin interaction
ENSG00000251872	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000226087	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1693864	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1693869	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723482	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1723483	0.98[ASN][1000 genomes]
rs1723493	0.95[ASN][1000 genomes]
rs2454081	0.89[ASN][1000 genomes]
rs815807	0.91[ASN][1000 genomes]
rs815811	0.91[EUR][1000 genomes];0.89[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47404200-47406400	Weak transcription	Small Intestine	intestine
2	chr2:47404200-47410600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:47404400-47406200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:47404400-47406600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr2:47404400-47406600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr2:47404400-47406600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:47404400-47406600	Weak transcription	Spleen	Spleen
8	chr2:47404400-47406800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr2:47404400-47418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:47404600-47406200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:47404600-47406600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:47404600-47406800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:47404600-47406800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:47404600-47406800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr2:47404600-47406800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:47404600-47407600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr2:47404600-47416400	Weak transcription	HSMMtube	muscle
18	chr2:47404600-47417200	Weak transcription	Placenta	Placenta
19	chr2:47404800-47406400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr2:47404800-47406400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:47404800-47406400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:47404800-47406800	Enhancers	A549	lung
23	chr2:47404800-47406800	Enhancers	K562	blood
24	chr2:47404800-47407400	Enhancers	Primary B cells from cord blood	blood
25	chr2:47404800-47411000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:47404800-47411000	Weak transcription	NH-A	brain
27	chr2:47404800-47416400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:47405000-47406400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr2:47405000-47406400	Weak transcription	NHEK	skin
30	chr2:47405000-47407800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:47405000-47408000	Weak transcription	NHDF-Ad	bronchial
32	chr2:47405200-47406200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:47405200-47406400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:47405200-47406400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:47405200-47406400	Weak transcription	Fetal Thymus	thymus
36	chr2:47405200-47406400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:47405200-47406400	Weak transcription	GM12878-XiMat	blood
38	chr2:47405200-47406400	Weak transcription	HMEC	breast
39	chr2:47405200-47406600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:47405200-47411200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:47405400-47406400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:47405400-47416400	Weak transcription	Fetal Intestine Large	intestine
43	chr2:47405600-47406400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:47405600-47406600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:47405600-47406600	Weak transcription	Stomach Mucosa	stomach
46	chr2:47405600-47406800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:47405600-47408200	Weak transcription	Brain Anterior Caudate	brain
48	chr2:47405800-47406200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:47405800-47406600	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr2:47405800-47406800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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