Variant report

Variant	rs7601969
Chromosome Location	chr2:58272602-58272603
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr2:58272265-58273010	K562	blood:	n/a	n/a
2	POLR2A	chr2:58271722-58272616	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:58272024-58275047	GM18951	blood:	n/a	n/a
4	POLR2A	chr2:58271963-58275203	GM19193	blood:	n/a	n/a
5	POLR2A	chr2:58272318-58272607	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:58272171-58275631	GM18505	blood:	n/a	n/a
7	CHD1	chr2:58271698-58275822	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:58271724-58272699	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:58271924-58272610	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:58271253-58275620	GM12891	blood:	n/a	n/a
11	POLR2A	chr2:58271753-58275667	GM12878	blood:	n/a	n/a
12	TBP	chr2:58272185-58273059	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:58271686-58275020	GM12878	blood:	n/a	n/a
14	CTCF	chr2:58272581-58272628	K562	blood:	n/a	n/a
15	NFATC1	chr2:58272587-58274715	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:58133863..58138456-chr2:58272095..58275151,4	MCF-7	breast:
2	chr2:58133060..58135151-chr2:58272508..58275235,2	MCF-7	breast:
3	chr2:58258901..58260862-chr2:58271685..58273683,2	K562	blood:
4	chr2:58272245..58275889-chr2:58464232..58469335,5	K562	blood:

No data

Variant related genes	Relation type
VRK2	TF binding region
ENSG00000273063	Chromatin interaction
ENSG00000115392	Chromatin interaction
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs17049332	0.85[YRI][hapmap]
rs17049336	1.00[YRI][hapmap]
rs17049352	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs17049368	0.83[YRI][hapmap]
rs58150137	0.93[AFR][1000 genomes]
rs59350619	0.93[AFR][1000 genomes]
rs6733307	0.85[YRI][hapmap]
rs6744187	0.93[AFR][1000 genomes]
rs72949138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951080	0.86[AFR][1000 genomes]
rs72951097	0.86[AFR][1000 genomes]
rs7579768	1.00[YRI][hapmap];0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58256800-58272800	Weak transcription	Adipose Nuclei	Adipose
2	chr2:58256800-58273000	Weak transcription	Pancreas	Pancrea
3	chr2:58258400-58273000	Weak transcription	Liver	Liver
4	chr2:58258800-58273000	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:58260000-58272800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:58260400-58273400	Weak transcription	Ovary	ovary
7	chr2:58262200-58273000	Weak transcription	Psoas Muscle	Psoas
8	chr2:58263000-58272800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:58266600-58273000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:58266600-58273200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:58266800-58273400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:58268000-58273000	Weak transcription	Aorta	Aorta
13	chr2:58268000-58273200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:58268600-58273400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:58269200-58273000	Weak transcription	Esophagus	oesophagus
16	chr2:58269200-58273400	Weak transcription	Gastric	stomach
17	chr2:58270000-58272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:58270000-58272800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:58270000-58273000	Weak transcription	HSMM	muscle
20	chr2:58270000-58273400	Weak transcription	Fetal Brain Male	brain
21	chr2:58270200-58272800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:58270200-58273200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:58270400-58272800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:58270400-58272800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:58270400-58272800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:58270400-58272800	Weak transcription	NHEK	skin
27	chr2:58270400-58272800	Weak transcription	Osteobl	bone
28	chr2:58270400-58273000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:58270400-58273200	Weak transcription	NH-A	brain
30	chr2:58271200-58272800	Enhancers	HUVEC	blood vessel
31	chr2:58271400-58272800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr2:58271400-58273000	Enhancers	Primary B cells from peripheral blood	blood
33	chr2:58271600-58272800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:58271600-58273200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr2:58271600-58273400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:58271800-58272800	Enhancers	Brain Hippocampus Middle	brain
37	chr2:58271800-58273000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr2:58271800-58273000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:58271800-58273200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr2:58271800-58273200	Enhancers	Primary hematopoietic stem cells	blood
41	chr2:58271800-58273200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:58271800-58273200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr2:58271800-58273400	Enhancers	Left Ventricle	heart
44	chr2:58272000-58272800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr2:58272000-58272800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:58272000-58273000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr2:58272000-58273000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr2:58272000-58273000	Enhancers	Right Ventricle	heart
49	chr2:58272000-58273200	Enhancers	Primary T cells from cord blood	blood
50	chr2:58272000-58273200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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