Variant report

Variant	rs2077921
Chromosome Location	chr2:173298008-173298009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr2:173297999-173298173	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr2:173297999-173298199	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:173297906-173298938	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:173291261..173294444-chr2:173294873..173298615,3	K562	blood:
2	chr2:173291662..173294325-chr2:173297442..173299980,3	MCF-7	breast:
3	chr2:173291657..173293814-chr2:173297316..173300145,3	MCF-7	breast:
4	chr2:173291236..173294444-chr2:173296195..173299585,6	K562	blood:
5	chr2:173297263..173301573-chr2:173305902..173308346,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLX2-9	chr2:173296163-173300407	ucscGeneNc_uc002uht_1

No data

Variant related genes	Relation type
ENSG00000226963	TF binding region
ENSG00000226963	Chromatin interaction
ENSG00000091409	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10184567	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs28464102	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28540552	0.85[ASN][1000 genomes]
rs7567159	0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7604441	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2077921	HOXD9	cis	parietal	SCAN
rs2077921	UBR3	cis	cerebellum	SCAN
rs2077921	DHRS9	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173294000-173301800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:173294200-173302600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:173294400-173299200	Weak transcription	Placenta	Placenta
4	chr2:173294400-173301400	Weak transcription	Aorta	Aorta
5	chr2:173294600-173302400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:173294600-173302600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:173294600-173302600	Weak transcription	NH-A	brain
8	chr2:173294600-173303000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:173294600-173303400	Weak transcription	NHLF	lung
10	chr2:173294800-173298200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:173294800-173298200	Enhancers	HepG2	liver
12	chr2:173294800-173299600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:173294800-173299800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:173294800-173302400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:173294800-173302400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:173294800-173306400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:173294800-173308800	Enhancers	Stomach Mucosa	stomach
18	chr2:173295000-173298600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:173295000-173299000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:173295000-173299400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:173295000-173299400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:173295000-173300800	Enhancers	Primary hematopoietic stem cells	blood
23	chr2:173295000-173301200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr2:173295000-173302200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:173295000-173303800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:173295200-173299400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:173295200-173302600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:173295200-173306600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:173295200-173306600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr2:173295400-173298600	Enhancers	Fetal Intestine Small	intestine
31	chr2:173295600-173299400	Enhancers	Brain Hippocampus Middle	brain
32	chr2:173295600-173299800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr2:173295600-173301600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:173295600-173308600	Enhancers	Fetal Intestine Large	intestine
35	chr2:173295800-173298400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:173295800-173299400	Enhancers	Psoas Muscle	Psoas
37	chr2:173295800-173302400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:173296000-173298600	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr2:173296000-173299000	Weak transcription	A549	lung
40	chr2:173296000-173299200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:173296000-173300600	Enhancers	Colonic Mucosa	Colon
42	chr2:173296000-173301800	Weak transcription	HSMM	muscle
43	chr2:173296000-173302400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr2:173296000-173305600	Weak transcription	Fetal Lung	lung
45	chr2:173296000-173307600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr2:173296200-173299800	Weak transcription	Right Ventricle	heart
47	chr2:173296200-173303800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:173296200-173305000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr2:173296200-173307600	Enhancers	Fetal Thymus	thymus
50	chr2:173296400-173298600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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