Variant report

Variant	rs73100939
Chromosome Location	chr1:226863874-226863875
allele	A/G
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:3)
LncRNA
region (count:1)
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	NFATC1	chr1:226863386-226864336	GM12878	blood:	n/a	n/a
2	YY1	chr1:226863750-226864044	GM12892	blood:	n/a	n/a
3	WRNIP1	chr1:226863666-226864101	GM12878	blood:	n/a	n/a
4	YY1	chr1:226863689-226864137	GM12878	blood:	n/a	n/a
5	NFATC1	chr1:226863585-226864068	GM12878	blood:	n/a	n/a
6	BHLHE40	chr1:226863762-226864460	GM12878	blood:	n/a	n/a
7	YY1	chr1:226863780-226864088	GM12878	blood:	n/a	n/a
8	RUNX3	chr1:226863646-226864609	GM12878	blood:	n/a	n/a
9	EP300	chr1:226863722-226864475	GM12878	blood:	n/a	n/a
10	YY1	chr1:226863770-226864071	GM12891	blood:	n/a	n/a
11	YY1	chr1:226863816-226864061	GM12892	blood:	n/a	n/a
12	MXI1	chr1:226863776-226864318	GM12878	blood:	n/a	n/a
13	EP300	chr1:226863817-226864428	GM12878	blood:	n/a	n/a
14	MTA3	chr1:226863492-226864520	GM12878	blood:	n/a	n/a
15	RUNX3	chr1:226863694-226864559	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:226848680..226852398-chr1:226863556..226867477,3	MCF-7	breast:
2	chr1:226858880..226860539-chr1:226862980..226865164,2	K562	blood:
3	chr1:226863575..226866275-chr1:226866512..226868016,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf95-1	chr1:226863815-226864046	ENSG00000228548.1

No data

Variant related genes	Relation type
ITPKB-IT1	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12065094	1.00[AMR][1000 genomes]
rs12095028	0.90[AFR][1000 genomes]
rs4653461	0.93[AFR][1000 genomes]
rs58755194	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73100937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73100938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73100942	0.95[AFR][1000 genomes];1.00[AMR][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	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226851800-226864000	Weak transcription	HMEC	breast
2	chr1:226852200-226864000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:226853000-226864800	Weak transcription	Pancreas	Pancrea
4	chr1:226853200-226864600	Weak transcription	Ovary	ovary
5	chr1:226854000-226864600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:226854800-226864800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:226855200-226864600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:226856200-226864600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:226856200-226864600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:226856200-226867400	Weak transcription	Fetal Brain Female	brain
11	chr1:226856200-226868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:226859600-226864400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:226859600-226867600	Enhancers	Colon Smooth Muscle	Colon
14	chr1:226860000-226864600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr1:226860200-226867000	Enhancers	Left Ventricle	heart
16	chr1:226860400-226864000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:226860400-226864600	Enhancers	Brain Substantia Nigra	brain
18	chr1:226860400-226866200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:226860600-226865200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:226860600-226867600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:226860600-226867600	Weak transcription	Gastric	stomach
22	chr1:226860800-226867400	Weak transcription	Fetal Intestine Large	intestine
23	chr1:226860800-226867400	Weak transcription	Fetal Intestine Small	intestine
24	chr1:226861600-226865600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr1:226861600-226866800	Enhancers	Psoas Muscle	Psoas
26	chr1:226861600-226867400	Enhancers	Fetal Muscle Leg	muscle
27	chr1:226862200-226864600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr1:226862200-226866800	Enhancers	Lung	lung
29	chr1:226862400-226864000	Enhancers	Colonic Mucosa	Colon
30	chr1:226862400-226864200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr1:226862400-226864800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:226862400-226865600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr1:226862400-226865600	Flanking Active TSS	GM12878-XiMat	blood
34	chr1:226862400-226865800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:226862400-226866000	Enhancers	NHDF-Ad	bronchial
36	chr1:226862400-226866800	Enhancers	Right Atrium	heart
37	chr1:226862400-226867000	Enhancers	Spleen	Spleen
38	chr1:226862400-226867600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:226862400-226867600	Enhancers	Placenta	Placenta
40	chr1:226862400-226868400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr1:226862600-226864600	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:226862600-226864800	Enhancers	H1 Cell Line	embryonic stem cell
43	chr1:226862600-226865600	Enhancers	NHLF	lung
44	chr1:226862600-226865800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:226862600-226866200	Enhancers	Esophagus	oesophagus
46	chr1:226862600-226867200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:226862600-226867400	Enhancers	Brain Angular Gyrus	brain
48	chr1:226862600-226867600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:226862800-226864600	Enhancers	Brain Anterior Caudate	brain
50	chr1:226862800-226866400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links