Variant report

Variant	rs11119988
Chromosome Location	chr1:212788206-212788207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:212778466-212788906	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr1:212787830-212788437	GM12878	blood:	n/a	chr1:212788220-212788234
3	FOXM1	chr1:212787584-212788442	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:212787958-212789681	K562	blood:	n/a	n/a
5	POLR2A	chr1:212787984-212788644	GM12892	blood:	n/a	n/a
6	ZNF143	chr1:212788076-212788480	GM12878	blood:	n/a	n/a
7	RUNX3	chr1:212787358-212788541	GM12878	blood:	n/a	n/a
8	ZNF384	chr1:212787659-212788353	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:212779324-212788938	Hela-S3	cervix:	n/a	n/a
10	YY1	chr1:212787855-212788391	GM12891	blood:	n/a	n/a
11	CHD1	chr1:212779286-212788865	IMR90	lung:	n/a	chr1:212783477-212783487 chr1:212782811-212782821
12	MAZ	chr1:212788056-212788475	GM12878	blood:	n/a	n/a
13	BHLHE40	chr1:212787857-212788283	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:212780020-212789160	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:212788084-212788484	GM12891	blood:	n/a	n/a
16	POLR2A	chr1:212787946-212789828	Hela-S3	cervix:	n/a	n/a
17	EP300	chr1:212788016-212788374	GM12878	blood:	n/a	chr1:212788220-212788234
18	RUNX3	chr1:212787884-212788425	GM12878	blood:	n/a	n/a
19	YY1	chr1:212787846-212788331	GM12892	blood:	n/a	n/a
20	YY1	chr1:212787843-212788384	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:212787917-212788699	GM12892	blood:	n/a	n/a
22	MEF2A	chr1:212787295-212788424	GM12878	blood:	n/a	n/a
23	NFIC	chr1:212787362-212788392	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:212788022-212788936	K562	blood:	n/a	n/a
25	MXI1	chr1:212787788-212788300	GM12878	blood:	n/a	n/a
26	TAF1	chr1:212787970-212788360	GM12878	blood:	n/a	n/a
27	NFIC	chr1:212787493-212788443	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:212781346-212789662	HepG2	liver:	n/a	n/a
29	MTA3	chr1:212787268-212788528	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:212780144-212798001	IMR90	lung:	n/a	n/a
31	CHD2	chr1:212788135-212788455	GM12878	blood:	n/a	n/a
32	ATF2	chr1:212787408-212788460	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:212787968-212791124	GM12878	blood:	n/a	n/a
34	MEF2A	chr1:212787744-212788318	GM12878	blood:	n/a	n/a
35	TBL1XR1	chr1:212788030-212788430	GM12878	blood:	n/a	n/a
36	YY1	chr1:212787904-212788404	GM12892	blood:	n/a	n/a
37	POLR2A	chr1:212788106-212789627	Hela-S3	cervix:	n/a	n/a
38	YY1	chr1:212787872-212788474	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:212787939-212789307	GM12878	blood:	n/a	n/a
40	YY1	chr1:212787912-212788250	K562	blood:	n/a	n/a
41	POLR2A	chr1:212782514-212798502	A549	lung:	n/a	n/a
42	POLR2A	chr1:212787940-212789004	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:212785851..212789357-chr1:212837777..212840991,5	K562	blood:
2	chr1:212780951..212783971-chr1:212784548..212788701,9	MCF-7	breast:
3	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
4	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:

No data

Variant related genes	Relation type
ATF3	TF binding region
ENSG00000162772	Chromatin interaction
ENSG00000260805	Chromatin interaction
ENSG00000237980	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1126526	0.80[CEU][hapmap]
rs4951627	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9429888	0.80[CEU][hapmap];0.81[EUR][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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11119988	CD46	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212783400-212790400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:212783400-212791600	Weak transcription	Ovary	ovary
3	chr1:212783600-212792000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:212784000-212792000	Weak transcription	Esophagus	oesophagus
5	chr1:212784000-212794200	Weak transcription	HUVEC	blood vessel
6	chr1:212784200-212788400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:212784200-212788600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:212784200-212788600	Weak transcription	Fetal Intestine Large	intestine
9	chr1:212784200-212789200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:212784200-212790400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:212784200-212796800	Weak transcription	Stomach Mucosa	stomach
12	chr1:212784400-212788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:212784400-212790200	Weak transcription	Dnd41	blood
14	chr1:212784400-212790400	Weak transcription	Colonic Mucosa	Colon
15	chr1:212784600-212788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:212784600-212788400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:212784600-212788400	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:212784600-212788400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:212784600-212788400	Weak transcription	NHEK	skin
20	chr1:212784600-212788800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:212784800-212788400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:212784800-212790400	Weak transcription	Brain Angular Gyrus	brain
23	chr1:212784800-212794800	Weak transcription	NH-A	brain
24	chr1:212785000-212788400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:212785000-212788400	Weak transcription	Hela-S3	cervix
26	chr1:212785000-212788600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:212785000-212790200	Weak transcription	Psoas Muscle	Psoas
28	chr1:212785000-212797000	Weak transcription	Right Atrium	heart
29	chr1:212785000-212801000	Weak transcription	Fetal Heart	heart
30	chr1:212785200-212788400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:212785400-212790000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:212785400-212795600	Weak transcription	A549	lung
33	chr1:212785800-212788400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:212785800-212792400	Weak transcription	Small Intestine	intestine
35	chr1:212786000-212788400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:212786000-212788400	Weak transcription	Brain Anterior Caudate	brain
37	chr1:212786400-212794000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:212786600-212788400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:212786600-212788800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:212786600-212790200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:212786600-212795200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:212786800-212788400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:212786800-212791600	Weak transcription	Fetal Lung	lung
44	chr1:212787000-212794000	Strong transcription	Fetal Intestine Small	intestine
45	chr1:212787000-212794400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr1:212787200-212788600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:212787200-212788600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr1:212787200-212788600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:212787200-212788600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:212787200-212791600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links