Variant report

Variant	rs11670761
Chromosome Location	chr19:19649327-19649328
allele	C/G
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	CTCF	chr19:19649200-19649350	GM12875	blood:	n/a	n/a
2	POLR2A	chr19:19648792-19649430	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr19:19648861-19649427	ECC-1	luminal epithelium:	n/a	chr19:19649059-19649069
4	POLR2A	chr19:19648645-19649334	ECC-1	luminal epithelium:	n/a	n/a
5	MAZ	chr19:19648707-19649977	IMR90	lung:	n/a	chr19:19649515-19649525 chr19:19649059-19649069
6	ZBTB7A	chr19:19648693-19649711	ECC-1	luminal epithelium:	n/a	chr19:19649367-19649378
7	POLR2A	chr19:19648629-19649404	H1-hESC	embryonic stem cell:	n/a	n/a
8	PBX3	chr19:19648675-19649356	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr19:19648680-19649483	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZBTB7A	chr19:19648724-19649713	ECC-1	luminal epithelium:	n/a	chr19:19649367-19649378
11	MXI1	chr19:19649097-19649344	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19647870..19650487-chr19:19773815..19776020,2	MCF-7	breast:
2	chr19:19648360..19650075-chr19:19737805..19740650,3	MCF-7	breast:
3	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:
4	chr19:19647280..19649688-chr19:19752870..19754432,2	MCF-7	breast:
5	chr19:19625665..19627306-chr19:19648287..19650892,2	K562	blood:

Variant related genes	Relation type
CILP2	TF binding region
ENSG00000089639	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000178093	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1036215	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10406278	0.82[EUR][1000 genomes]
rs11085264	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11668203	0.89[EUR][1000 genomes]
rs11669558	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11669730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670687	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670882	0.95[EUR][1000 genomes]
rs11671253	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1560687	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16996127	0.99[EUR][1000 genomes]
rs17684164	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060274	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2060275	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905434	0.81[EUR][1000 genomes]
rs2916070	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2916072	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2916075	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965179	0.85[EUR][1000 genomes]
rs2965181	0.85[EUR][1000 genomes]
rs2965184	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965186	0.81[EUR][1000 genomes]
rs34487417	0.83[EUR][1000 genomes]
rs34667451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45556231	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45631651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808204	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808205	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808206	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808951	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808958	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808962	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808970	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55927782	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56280531	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56291054	0.83[EUR][1000 genomes]
rs56330647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58074958	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61744761	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7245689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7250233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7252453	0.96[EUR][1000 genomes]
rs7256028	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs751857	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754256	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8100927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101219	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102502	0.94[EUR][1000 genomes]
rs8105642	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110171	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8110250	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8111093	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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv911307	chr19:19631655-19657143	Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11670761	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19630600-19651800	Weak transcription	A549	lung
2	chr19:19642200-19650600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:19646600-19649600	Weak transcription	Brain Angular Gyrus	brain
5	chr19:19647800-19650000	Enhancers	Spleen	Spleen
6	chr19:19648000-19649800	Bivalent Enhancer	Fetal Intestine Large	intestine
7	chr19:19648000-19649800	Enhancers	Pancreas	Pancrea
8	chr19:19648200-19649400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
9	chr19:19648200-19649600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:19648200-19649600	Enhancers	Gastric	stomach
11	chr19:19648200-19649800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
12	chr19:19648200-19650000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr19:19648200-19650000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:19648200-19650000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr19:19648200-19650000	Bivalent Enhancer	Fetal Thymus	thymus
16	chr19:19648200-19650000	Enhancers	Lung	lung
17	chr19:19648200-19651400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr19:19648200-19651600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr19:19648400-19649800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr19:19648400-19649800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr19:19648400-19650000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:19648400-19650000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
23	chr19:19648400-19650200	Bivalent Enhancer	Placenta	Placenta
24	chr19:19648400-19651400	Bivalent Enhancer	Fetal Stomach	stomach
25	chr19:19648600-19649400	Bivalent Enhancer	Brain Anterior Caudate	brain
26	chr19:19648600-19649400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
27	chr19:19648600-19649800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr19:19648600-19649800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr19:19648600-19649800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr19:19648600-19649800	Bivalent Enhancer	Fetal Intestine Small	intestine
31	chr19:19648600-19649800	Bivalent Enhancer	Stomach Mucosa	stomach
32	chr19:19648600-19650000	Bivalent Enhancer	Primary T cells from cord blood	blood
33	chr19:19648600-19650000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:19648600-19650000	Bivalent Enhancer	Adipose Nuclei	Adipose
35	chr19:19648600-19650000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
36	chr19:19648600-19650200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:19648800-19649400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr19:19648800-19649400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr19:19648800-19649400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
40	chr19:19648800-19649400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:19648800-19649400	Bivalent Enhancer	Liver	Liver
42	chr19:19648800-19649400	Enhancers	Brain Cingulate Gyrus	brain
43	chr19:19648800-19649400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr19:19648800-19649400	Bivalent Enhancer	Brain Substantia Nigra	brain
45	chr19:19648800-19649400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
46	chr19:19648800-19649400	Flanking Bivalent TSS/Enh	Thymus	Thymus
47	chr19:19648800-19649600	Active TSS	H9 Cell Line	embryonic stem cell
48	chr19:19648800-19649600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr19:19648800-19649600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
50	chr19:19648800-19649600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links