Variant report

Variant	rs6426156
Chromosome Location	chr1:224921487-224921488
allele	C/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	POLR2A	chr1:224920656-224921696	U87	brain:	n/a	n/a
2	CTCF	chr1:224921360-224921510	BE2_C	brain:	n/a	chr1:224921486-224921499
3	RELA	chr1:224920506-224921505	GM12878	blood:	n/a	n/a
4	EP300	chr1:224920626-224921875	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:224920810-224921501	H1-neurons	neurons:	n/a	n/a
6	EP300	chr1:224920469-224921943	GM12878	blood:	n/a	n/a
7	IKZF1	chr1:224920525-224921635	GM12878	blood:	n/a	n/a
8	CTCF	chr1:224921400-224921550	GM12875	blood:	n/a	chr1:224921486-224921499
9	EBF1	chr1:224920580-224921839	GM12878	blood:	n/a	chr1:224921507-224921518 chr1:224921508-224921517 chr1:224921541-224921554 chr1:224921543-224921553 chr1:224921541-224921552 chr1:224921543-224921552 chr1:224921543-224921552
10	CTCF	chr1:224921400-224921550	GM12871	blood:	n/a	chr1:224921486-224921499
11	YY1	chr1:224921184-224921523	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:224920657-224921688	GM12892	blood:	n/a	n/a
13	CTCF	chr1:224921400-224921550	GM12864	blood:	n/a	chr1:224921486-224921499
14	WRNIP1	chr1:224920309-224922464	GM12878	blood:	n/a	n/a
15	RELA	chr1:224920305-224921679	GM18951	blood:	n/a	n/a
16	RUNX3	chr1:224920591-224921555	GM12878	blood:	n/a	chr1:224921078-224921095
17	POLR2A	chr1:224920712-224921747	U87	brain:	n/a	n/a
18	RFX5	chr1:224920619-224921663	SK-N-SH	brain:	n/a	n/a
19	MAX	chr1:224920495-224921875	GM12878	blood:	n/a	chr1:224921619-224921630
20	MXI1	chr1:224920533-224921795	GM12878	blood:	n/a	n/a
21	BHLHE40	chr1:224920673-224921861	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:224920736-224921594	U87	brain:	n/a	n/a
23	SPI1	chr1:224921257-224921610	GM12878	blood:	n/a	n/a
24	RCOR1	chr1:224920522-224921833	GM12878	blood:	n/a	n/a
25	CTCF	chr1:224921380-224921530	GM12864	blood:	n/a	chr1:224921486-224921499
26	REST	chr1:224920778-224921701	H1-neurons	neurons:	n/a	chr1:224921331-224921344
27	POLR2A	chr1:224920650-224921702	U87	brain:	n/a	n/a
28	POLR2A	chr1:224920833-224921489	H1-neurons	neurons:	n/a	n/a
29	EBF1	chr1:224921301-224921734	GM12878	blood:	n/a	chr1:224921507-224921518 chr1:224921508-224921517 chr1:224921541-224921554 chr1:224921543-224921553 chr1:224921541-224921552 chr1:224921543-224921552 chr1:224921543-224921552
30	GATA2	chr1:224920869-224921720	SH-SY5Y	brain:	n/a	chr1:224921200-224921217
31	CTCF	chr1:224921420-224921570	GM12872	blood:	n/a	chr1:224921486-224921499
32	EBF1	chr1:224920381-224922593	GM12878	blood:	n/a	chr1:224921507-224921518 chr1:224921508-224921517 chr1:224921541-224921554 chr1:224921543-224921553 chr1:224921541-224921552 chr1:224921543-224921552 chr1:224921543-224921552
33	CTCF	chr1:224921340-224921490	HBMEC	blood vessel:	n/a	n/a
34	SMC3	chr1:224920410-224921757	GM12878	blood:	n/a	n/a
35	RUNX3	chr1:224921258-224921619	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:224920616-224921798	GM12892	blood:	n/a	n/a
37	TBP	chr1:224920496-224921847	GM12878	blood:	n/a	n/a
38	CHD2	chr1:224920202-224921848	GM12878	blood:	n/a	n/a
39	PBX3	chr1:224921362-224921555	GM12878	blood:	n/a	n/a
40	CTCF	chr1:224921026-224921724	GM12878	blood:	n/a	chr1:224921486-224921499
41	BATF	chr1:224921246-224921615	GM12878	blood:	n/a	chr1:224921428-224921439
42	PAX5	chr1:224920615-224921782	GM12878	blood:	n/a	n/a
43	CTCF	chr1:224921360-224921510	GM12873	blood:	n/a	chr1:224921486-224921499
44	STAT3	chr1:224920538-224921730	GM12878	blood:	n/a	chr1:224921237-224921249
45	YY1	chr1:224920768-224921572	GM12892	blood:	n/a	n/a
46	RELA	chr1:224920585-224921693	GM19099	blood:	n/a	n/a
47	TCF12	chr1:224921259-224921846	GM12878	blood:	n/a	n/a
48	TBL1XR1	chr1:224920319-224921816	GM12878	blood:	n/a	n/a
49	EP300	chr1:224920683-224921650	GM12878	blood:	n/a	n/a
50	CTCF	chr1:224921340-224921490	GM12865	blood:	n/a	n/a

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	chr1:224920081..224922903-chr1:224922930..224927181,4	MCF-7	breast:
5	chr1:224912065..224916127-chr1:224919460..224922896,4	MCF-7	breast:

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

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2005073	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:58 , 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	chr1:224917400-224921600	Enhancers	NHDF-Ad	bronchial
5	chr1:224918200-224921800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:224918400-224924600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:224919000-224923200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:224919600-224926200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:224919800-224921600	Enhancers	Pancreas	Pancrea
10	chr1:224919800-224921800	Enhancers	Esophagus	oesophagus
11	chr1:224919800-224921800	Enhancers	Fetal Intestine Small	intestine
12	chr1:224919800-224922400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:224919800-224922800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:224920000-224921600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:224920000-224921800	Enhancers	HMEC	breast
16	chr1:224920000-224922200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr1:224920200-224921600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:224920200-224921600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:224920200-224921600	Enhancers	Adipose Nuclei	Adipose
20	chr1:224920200-224921600	Enhancers	Fetal Intestine Large	intestine
21	chr1:224920200-224921800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:224920200-224921800	Enhancers	Right Atrium	heart
23	chr1:224920200-224921800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr1:224920200-224921800	Enhancers	Osteobl	bone
25	chr1:224920200-224922000	Enhancers	Right Ventricle	heart
26	chr1:224920200-224922400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:224920200-224923400	Enhancers	Fetal Thymus	thymus
28	chr1:224920200-224924200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:224920200-224925000	Weak transcription	Colonic Mucosa	Colon
30	chr1:224920400-224921600	Enhancers	Duodenum Mucosa	Duodenum
31	chr1:224920400-224921600	Enhancers	Placenta	Placenta
32	chr1:224920400-224921600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr1:224920400-224921800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:224920400-224922200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:224920400-224922200	Flanking Active TSS	GM12878-XiMat	blood
36	chr1:224920400-224922400	Enhancers	Left Ventricle	heart
37	chr1:224920400-224922800	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr1:224920600-224921600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr1:224920800-224921600	Enhancers	Fetal Lung	lung
40	chr1:224921000-224921600	Enhancers	NHEK	skin
41	chr1:224921000-224921800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:224921000-224922400	Enhancers	Liver	Liver
43	chr1:224921000-224922800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:224921000-224924200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:224921200-224921600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr1:224921200-224921800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:224921200-224921800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:224921200-224921800	Bivalent Enhancer	Fetal Stomach	stomach
49	chr1:224921200-224922200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:224921200-224922800	Strong transcription	Dnd41	blood

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