Variant report

Variant	rs11669730
Chromosome Location	chr19:19648713-19648714
allele	A/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	POLR2A	chr19:19648626-19649266	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr19:19648689-19649184	HEK293-T-REx	kidney:	n/a	n/a
3	POLR2A	chr19:19648645-19649334	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr19:19648681-19649116	GM12892	blood:	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	MTA3	chr19:19648680-19649174	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:19648629-19649404	H1-hESC	embryonic stem cell:	n/a	n/a
9	SP1	chr19:19648688-19649253	H1-hESC	embryonic stem cell:	n/a	chr19:19649009-19649019 chr19:19649025-19649035 chr19:19649056-19649068 chr19:19649058-19649067 chr19:19649008-19649020 chr19:19649008-19649020 chr19:19649025-19649035 chr19:19649057-19649071 chr19:19649009-19649019
10	PBX3	chr19:19648675-19649356	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr19:19648648-19649210	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr19:19648680-19649483	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:19648655-19649125	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:19648670-19649199	GM12891	blood:	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	chr19:19647280..19649688-chr19:19752870..19754432,2	MCF-7	breast:
4	chr19:19625665..19627306-chr19:19648287..19650892,2	K562	blood:
5	chr19:19641380..19649124-chr19:19737025..19742358,12	MCF-7	breast:

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

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1005372	1.00[CHD][hapmap]
rs1036215	0.88[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10406278	0.82[EUR][1000 genomes]
rs10421328	1.00[CHD][hapmap]
rs11085264	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];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]
rs11670687	0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670775	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670882	0.82[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs11671253	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12977072	1.00[CHD][hapmap]
rs1560687	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16996127	0.88[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17684164	0.88[CEU][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060274	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2060275	0.88[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905434	0.81[EUR][1000 genomes]
rs2916070	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];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	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965186	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs2965190	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs2965195	0.88[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap]
rs2965201	0.80[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
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[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808951	0.88[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808958	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808962	0.93[CEU][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808968	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];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	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[GIH][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7252453	0.82[CEU][hapmap];0.96[EUR][1000 genomes]
rs7253821	1.00[CHD][hapmap]
rs7256028	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs751857	1.00[ASW][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754256	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs756997	0.88[CEU][hapmap]
rs8100927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101219	0.91[ASW][hapmap];0.88[GIH][hapmap];0.94[LWK][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102502	0.82[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs8105642	0.88[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8108180	1.00[CHD][hapmap]
rs8110171	0.88[CEU][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8110250	0.88[CEU][hapmap];0.83[YRI][hapmap];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
rs11669730	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19630600-19651800	Weak transcription	A549	lung
2	chr19:19635200-19649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:19638400-19648800	Weak transcription	GM12878-XiMat	blood
4	chr19:19642200-19650600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:19643400-19648800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:19643600-19648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:19643600-19648800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:19643800-19648800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:19643800-19648800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:19643800-19648800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:19643800-19648800	Weak transcription	Right Atrium	heart
13	chr19:19643800-19649000	Weak transcription	Left Ventricle	heart
14	chr19:19644200-19649000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:19644200-19649000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:19645400-19648800	Weak transcription	Fetal Heart	heart
17	chr19:19645600-19648800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:19645600-19648800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:19646600-19649600	Weak transcription	Brain Angular Gyrus	brain
20	chr19:19646800-19649000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:19647000-19648800	Weak transcription	Right Ventricle	heart
22	chr19:19647200-19648800	Weak transcription	Brain Hippocampus Middle	brain
23	chr19:19647800-19650000	Enhancers	Spleen	Spleen
24	chr19:19648000-19648800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:19648000-19648800	Active TSS	Ovary	ovary
26	chr19:19648000-19649800	Bivalent Enhancer	Fetal Intestine Large	intestine
27	chr19:19648000-19649800	Enhancers	Pancreas	Pancrea
28	chr19:19648200-19648800	Enhancers	Primary B cells from cord blood	blood
29	chr19:19648200-19648800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr19:19648200-19648800	Enhancers	HMEC	breast
31	chr19:19648200-19649000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:19648200-19649000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
33	chr19:19648200-19649000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:19648200-19649200	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr19:19648200-19649200	Bivalent Enhancer	NH-A	brain
36	chr19:19648200-19649400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
37	chr19:19648200-19649600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:19648200-19649600	Enhancers	Gastric	stomach
39	chr19:19648200-19649800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
40	chr19:19648200-19650000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr19:19648200-19650000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:19648200-19650000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr19:19648200-19650000	Bivalent Enhancer	Fetal Thymus	thymus
44	chr19:19648200-19650000	Enhancers	Lung	lung
45	chr19:19648200-19651400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
46	chr19:19648200-19651600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr19:19648400-19648800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:19648400-19648800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr19:19648400-19648800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:19648400-19648800	Bivalent/Poised TSS	Colonic Mucosa	Colon

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