Variant report

Variant	rs12465704
Chromosome Location	chr2:173422385-173422386
allele	A/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	WRNIP1	chr2:173421333-173422404	GM12878	blood:	n/a	n/a
2	MXI1	chr2:173418707-173422487	SK-N-SH	brain:	n/a	n/a
3	RCOR1	chr2:173422206-173422504	K562	blood:	n/a	n/a
4	CHD1	chr2:173419826-173422564	IMR90	lung:	n/a	n/a
5	MXI1	chr2:173419455-173422388	IMR90	lung:	n/a	n/a
6	GATA1	chr2:173416948-173422428	PBDE	blood:	n/a	chr2:173421509-173421522

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172966170..172969056-chr2:173419829..173422762,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225205	TF binding region
ENSG00000236651	Chromatin interaction
ENSG00000115844	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10181851	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1075638	0.82[EUR][1000 genomes]
rs10930562	0.87[EUR][1000 genomes]
rs10930565	0.87[EUR][1000 genomes]
rs3765065	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769321	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62167835	0.87[EUR][1000 genomes]
rs6710129	0.87[EUR][1000 genomes]
rs6738196	0.87[EUR][1000 genomes]
rs6752386	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	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	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv3035	chr2:173419058-173463901	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173419000-173423400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:173419200-173422400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:173419800-173422600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:173419800-173423400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr2:173420000-173422800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:173420000-173422800	Active TSS	Placenta Amnion	Placenta Amnion
7	chr2:173420000-173423000	Active TSS	GM12878-XiMat	blood
8	chr2:173420200-173422400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:173420200-173422400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:173420200-173422600	Active TSS	Hela-S3	cervix
11	chr2:173420400-173422400	Bivalent/Poised TSS	HepG2	liver
12	chr2:173421200-173422400	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr2:173421200-173422600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr2:173421400-173422400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:173421400-173422400	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr2:173421400-173422800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr2:173421400-173423000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr2:173421400-173423200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr2:173421400-173423200	Flanking Active TSS	Dnd41	blood
20	chr2:173421400-173423200	Flanking Active TSS	NHEK	skin
21	chr2:173421400-173423400	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr2:173421400-173436200	Weak transcription	Spleen	Spleen
23	chr2:173421600-173422400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:173421600-173422400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr2:173421600-173422600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr2:173421600-173422600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr2:173421600-173422800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:173421600-173423400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr2:173421600-173423400	Transcr. at gene 5' and 3'	K562	blood
30	chr2:173421600-173423400	Flanking Active TSS	NHDF-Ad	bronchial
31	chr2:173421600-173426000	Weak transcription	Esophagus	oesophagus
32	chr2:173421600-173427200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:173421600-173430000	Weak transcription	Gastric	stomach
34	chr2:173421600-173431000	Weak transcription	Aorta	Aorta
35	chr2:173421600-173436000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:173421600-173436000	Weak transcription	Lung	lung
37	chr2:173421600-173453400	Weak transcription	Pancreas	Pancrea
38	chr2:173421800-173422400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr2:173421800-173422600	Enhancers	Brain Substantia Nigra	brain
40	chr2:173421800-173422600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:173421800-173422800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr2:173421800-173423000	Active TSS	H1 Cell Line	embryonic stem cell
43	chr2:173421800-173423000	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr2:173421800-173423000	Enhancers	Primary B cells from peripheral blood	blood
45	chr2:173421800-173423000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:173421800-173423200	Weak transcription	Left Ventricle	heart
47	chr2:173421800-173423400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr2:173421800-173423400	Enhancers	Fetal Kidney	kidney
49	chr2:173421800-173423400	Flanking Active TSS	HMEC	breast
50	chr2:173421800-173423600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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