Variant report

Variant	rs11973674
Chromosome Location	chr7:5950901-5950902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs3094962	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
2	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
3	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
5	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
6	nsv1034215	chr7:5748982-6056619	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv1016690	chr7:5749222-6056619	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
8	nsv1027679	chr7:5760731-6056619	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv887420	chr7:5801820-5963545	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
11	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
12	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
13	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
14	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
15	nsv830892	chr7:5842044-5995489	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv433017	chr7:5853557-6045391	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv1024675	chr7:5868561-5965441	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1017061	chr7:5885326-6026706	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1031583	chr7:5889011-5970922	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv830894	chr7:5889658-6072215	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
21	nsv1026461	chr7:5891977-5970922	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv981428	chr7:5899882-5954957	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	esv1834433	chr7:5930582-5953089	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
24	nsv1034916	chr7:5934780-6158970	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
25	esv274969	chr7:5936888-5965441	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
26	esv1840621	chr7:5939594-5953089	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
27	esv2421482	chr7:5940039-5950934	Strong transcription Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
28	esv3477638	chr7:5948726-5953124	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
29	esv3477639	chr7:5948726-5953124	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
30	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11973674	FOXG1	trans	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5935200-5951600	Weak transcription	HMEC	breast
2	chr7:5938200-5952200	Weak transcription	NHDF-Ad	bronchial
3	chr7:5938200-5952400	Weak transcription	GM12878-XiMat	blood
4	chr7:5938200-5952600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:5938200-5955600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:5938200-5962800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:5938200-5963400	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:5938200-5969400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:5938400-5952200	Weak transcription	HepG2	liver
10	chr7:5938400-5952400	Weak transcription	Primary B cells from cord blood	blood
11	chr7:5938400-5952400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:5938400-5955600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:5938400-5955600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:5938400-5957800	Weak transcription	Aorta	Aorta
15	chr7:5938400-5963600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:5938400-5966600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:5938400-5966800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:5938400-5966800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:5938400-5967800	Weak transcription	HSMMtube	muscle
20	chr7:5938400-5971000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr7:5938400-5971400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:5938400-5972600	Weak transcription	Fetal Brain Female	brain
23	chr7:5938600-5962400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:5939600-5952200	Weak transcription	Small Intestine	intestine
25	chr7:5939600-5964200	Weak transcription	Brain Angular Gyrus	brain
26	chr7:5939800-5954600	Weak transcription	Fetal Heart	heart
27	chr7:5939800-5963200	Weak transcription	A549	lung
28	chr7:5939800-5966400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr7:5941200-5955200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr7:5941800-5952600	Strong transcription	Fetal Muscle Leg	muscle
31	chr7:5942600-5952200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr7:5943200-5951200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:5943200-5952800	Weak transcription	Fetal Lung	lung
34	chr7:5943400-5952000	Weak transcription	NHLF	lung
35	chr7:5943400-5971000	Weak transcription	Pancreas	Pancrea
36	chr7:5944200-5953200	Weak transcription	Psoas Muscle	Psoas
37	chr7:5944400-5962600	Weak transcription	Fetal Intestine Large	intestine
38	chr7:5944600-5963200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:5945400-5954800	Strong transcription	Fetal Intestine Small	intestine
40	chr7:5945400-5972600	Weak transcription	Gastric	stomach
41	chr7:5945600-5951000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:5945600-5951400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:5946200-5955200	Weak transcription	NHEK	skin
44	chr7:5946200-5955800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:5946400-5972400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:5947000-5969200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr7:5947200-5952400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:5947400-5962200	Weak transcription	Brain Hippocampus Middle	brain
49	chr7:5947600-5963400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr7:5947800-5953000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links