Variant report

Variant	rs13238780
Chromosome Location	chr7:6481624-6481625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6477471..6480538-chr7:6480717..6482413,3	K562	blood:
2	chr7:6479621..6482383-chr7:6485568..6487663,2	MCF-7	breast:
3	chr7:6478323..6480538-chr7:6480717..6482413,2	K562	blood:
4	chr7:6481582..6483120-chr7:6485839..6487647,2	K562	blood:
5	chr7:6475431..6480249-chr7:6480514..6484908,6	MCF-7	breast:
6	chr7:6480573..6483182-chr7:6515593..6518395,2	K562	blood:
7	chr7:6474528..6479669-chr7:6479864..6485085,5	MCF-7	breast:
8	chr7:6481370..6483042-chr7:6483146..6485535,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164535	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10239851	0.81[AMR][1000 genomes]
rs10281392	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs11767044	0.81[AMR][1000 genomes]
rs12112106	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs13309230	0.81[AMR][1000 genomes]
rs2689420	0.81[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs34054854	0.81[AMR][1000 genomes]
rs4724798	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs702483	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs702485	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs702486	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs73057348	0.95[ASN][1000 genomes]
rs755629	0.81[CHB][hapmap]
rs836477	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs836478	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs836480	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs836483	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs836498	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs836499	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836503	0.86[EUR][1000 genomes]
rs836508	0.92[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs836509	0.96[CEU][hapmap]
rs836513	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836516	0.82[ASW][hapmap];0.92[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs836526	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836527	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836529	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836534	0.92[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs836536	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836539	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836549	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs836551	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs836556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836558	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs861369	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1824738	chr7:6431933-6554222	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv1825865	chr7:6431933-6554222	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13238780	FSCN1	cis	cerebellum	SCAN
rs13238780	RAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6453000-6486800	Weak transcription	Small Intestine	intestine
2	chr7:6453600-6483200	Weak transcription	Fetal Kidney	kidney
3	chr7:6456800-6486800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:6465000-6486600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:6465800-6486400	Weak transcription	Colonic Mucosa	Colon
6	chr7:6466000-6486400	Weak transcription	Aorta	Aorta
7	chr7:6475400-6481800	Weak transcription	Brain Angular Gyrus	brain
8	chr7:6475400-6483200	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:6475400-6483400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:6475400-6484400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:6476000-6482000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:6476000-6484200	Weak transcription	K562	blood
13	chr7:6476200-6481800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:6476200-6486400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:6476400-6486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:6478200-6482600	Strong transcription	NHEK	skin
17	chr7:6478400-6485000	Strong transcription	Fetal Brain Female	brain
18	chr7:6478600-6483000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:6478800-6482800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:6478800-6485600	Strong transcription	Fetal Intestine Small	intestine
21	chr7:6478800-6486000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:6478800-6486600	Weak transcription	Fetal Heart	heart
23	chr7:6479000-6485400	Strong transcription	Fetal Intestine Large	intestine
24	chr7:6479000-6485400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr7:6479000-6486000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:6479200-6481800	Weak transcription	Adipose Nuclei	Adipose
27	chr7:6479200-6483000	Weak transcription	Right Ventricle	heart
28	chr7:6479200-6486400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:6479400-6481800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr7:6479400-6483000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:6479400-6483000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr7:6479400-6483000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:6479400-6486400	Weak transcription	Right Atrium	heart
34	chr7:6479600-6485600	Strong transcription	Fetal Muscle Leg	muscle
35	chr7:6479800-6481800	Strong transcription	A549	lung
36	chr7:6479800-6485800	Strong transcription	Fetal Thymus	thymus
37	chr7:6480000-6485600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr7:6480200-6482200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:6480400-6481800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:6480600-6482000	Strong transcription	Brain Germinal Matrix	brain
41	chr7:6480600-6485600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:6481000-6485800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr7:6481200-6482400	Genic enhancers	Placenta	Placenta
44	chr7:6481200-6485600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr7:6481200-6485800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr7:6481200-6486000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr7:6481200-6486000	Strong transcription	Fetal Stomach	stomach
48	chr7:6481400-6481800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:6481400-6481800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr7:6481400-6481800	Genic enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links