Variant report

Variant	rs2005073
Chromosome Location	chr1:224922767-224922768
allele	G/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	RUNX3	chr1:224922697-224923328	GM12878	blood:	n/a	n/a
2	CTCF	chr1:224922177-224922780	MCF-7	breast:	n/a	chr1:224922419-224922432 chr1:224922757-224922765 chr1:224922419-224922432 chr1:224922423-224922432
3	MAFK	chr1:224922648-224923338	GM12878	blood:	n/a	chr1:224922962-224922973 chr1:224922964-224922980 chr1:224922960-224922974 chr1:224922965-224922979 chr1:224922961-224922976 chr1:224922961-224922977 chr1:224922962-224922982
4	IKZF1	chr1:224922760-224923334	GM12878	blood:	n/a	n/a
5	CTCF	chr1:224922640-224922790	GM12864	blood:	n/a	chr1:224922757-224922765
6	NFIC	chr1:224922758-224923285	GM12878	blood:	n/a	n/a
7	CTCF	chr1:224922169-224922797	K562	blood:	n/a	chr1:224922419-224922432 chr1:224922757-224922765 chr1:224922419-224922432 chr1:224922423-224922432
8	SMC3	chr1:224922327-224922783	GM12878	blood:	n/a	chr1:224922419-224922429 chr1:224922422-224922430 chr1:224922425-224922433
9	CTCF	chr1:224922740-224922890	GM12864	blood:	n/a	chr1:224922757-224922765

No.	Distal block	Cell Line	Cell type
1	chr1:224921057..224922857-chr1:225011412..225013045,2	MCF-7	breast:
2	chr1:224917954..224920800-chr1:224921444..224923051,2	MCF-7	breast:
3	chr1:224920216..224922830-chr1:225115922..225118673,2	MCF-7	breast:
4	chr1:224922062..224922859-chr1:225040254..225041009,2	MCF-7	breast:
5	chr1:224920081..224922903-chr1:224922930..224927181,4	MCF-7	breast:
6	chr1:224832200..224833011-chr1:224921824..224922821,2	MCF-7	breast:
7	chr1:224912065..224916127-chr1:224919460..224922896,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229400	TF binding region
ENSG00000229400	Chromatin interaction
ENSG00000185842	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2802552	0.87[YRI][hapmap]
rs2802562	0.87[YRI][hapmap]
rs6426156	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6679040	0.90[CEU][hapmap]
rs72629698	0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524125	chr1:224902054-225021860	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224914800-224924400	Weak transcription	Ovary	ovary
2	chr1:224915000-224924400	Weak transcription	Brain Anterior Caudate	brain
3	chr1:224916200-224924200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:224918400-224924600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:224919000-224923200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:224919600-224926200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:224919800-224922800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:224920200-224923400	Enhancers	Fetal Thymus	thymus
9	chr1:224920200-224924200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:224920200-224925000	Weak transcription	Colonic Mucosa	Colon
11	chr1:224920400-224922800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:224921000-224922800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:224921000-224924200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:224921200-224922800	Strong transcription	Dnd41	blood
15	chr1:224921200-224924200	Weak transcription	Spleen	Spleen
16	chr1:224921400-224922800	Strong transcription	NHLF	lung
17	chr1:224921400-224924200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:224921400-224924400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:224921400-224924400	Weak transcription	NH-A	brain
20	chr1:224921600-224922800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:224921600-224923800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:224921600-224924200	Weak transcription	Adipose Nuclei	Adipose
23	chr1:224921600-224924400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:224921600-224924600	Weak transcription	Pancreas	Pancrea
25	chr1:224921600-224931400	Weak transcription	Psoas Muscle	Psoas
26	chr1:224921800-224922800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr1:224921800-224923600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:224921800-224923600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:224921800-224924200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:224921800-224924200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:224921800-224924200	Weak transcription	Osteobl	bone
32	chr1:224921800-224924400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:224921800-224924600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:224921800-224924600	Weak transcription	Right Atrium	heart
35	chr1:224921800-224925200	Weak transcription	Esophagus	oesophagus
36	chr1:224921800-224934600	Weak transcription	HMEC	breast
37	chr1:224922000-224923000	Strong transcription	NHDF-Ad	bronchial
38	chr1:224922000-224924600	Weak transcription	Right Ventricle	heart
39	chr1:224922200-224922800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:224922200-224923200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr1:224922200-224923400	Enhancers	Primary T cells from cord blood	blood
42	chr1:224922200-224923600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr1:224922200-224923600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:224922200-224923800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:224922200-224923800	Enhancers	GM12878-XiMat	blood
46	chr1:224922400-224923200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:224922400-224923200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr1:224922400-224923200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:224922400-224923200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:224922400-224924000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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