Variant report

Variant	rs3213506
Chromosome Location	chr4:3417484-3417485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3415712..3418675-chr4:3431596..3433223,2	MCF-7	breast:
2	chr4:3402341..3405091-chr4:3416697..3418981,2	MCF-7	breast:
3	chr4:3416652..3419915-chr4:3441173..3444245,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109758	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12644442	0.90[JPT][hapmap]
rs13109976	0.89[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13116176	0.81[JPT][hapmap]
rs13127597	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs13131192	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13152128	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1320762	0.90[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1320763	0.80[ASW][hapmap];0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1406674	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs1406675	0.81[JPT][hapmap]
rs16843157	0.94[CEU][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16844301	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16844307	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844309	0.90[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1730769	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17797467	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1894442	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1962767	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs3213507	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3748036	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752442	0.81[JPT][hapmap]
rs3789739	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4690090	0.89[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs4690093	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4690095	0.82[ASN][1000 genomes]
rs4690098	0.81[JPT][hapmap]
rs58143210	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274930	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6446740	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6828057	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs9790656	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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 target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv933265	chr4:3392824-4283640	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
11	esv2757918	chr4:3394344-4350986	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer 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	64 gene(s)	inside rSNPs	diseases
12	esv2759219	chr4:3394344-4350986	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
13	nsv461166	chr4:3405165-3451109	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv593450	chr4:3405165-3451109	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv878464	chr4:3405165-3505448	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv878465	chr4:3405165-3566567	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	esv1791851	chr4:3407753-3534022	Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv1000383	chr4:3412585-3839781	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	nsv461167	chr4:3413209-3446112	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv593451	chr4:3413209-3446112	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv461168	chr4:3413209-3449652	Genic enhancers Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv593452	chr4:3413209-3449652	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv878466	chr4:3413209-3451109	Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv878467	chr4:3413209-3454304	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv878468	chr4:3413209-3471754	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
26	nsv878469	chr4:3413209-3566567	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
27	nsv878470	chr4:3413209-3566567	Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
28	nsv878471	chr4:3413209-3884998	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
29	nsv878472	chr4:3414654-3451109	Weak transcription Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
30	nsv878473	chr4:3414654-3473139	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
31	esv1816543	chr4:3414654-3942867	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3213506	KIRREL3	trans	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3391800-3424200	Weak transcription	Colonic Mucosa	Colon
2	chr4:3399200-3432200	Weak transcription	Right Atrium	heart
3	chr4:3405200-3418800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:3407200-3417800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:3407400-3417800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:3407600-3418000	Weak transcription	Left Ventricle	heart
7	chr4:3407800-3417600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:3408800-3436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:3411000-3417800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:3411000-3436400	Strong transcription	Fetal Intestine Small	intestine
11	chr4:3411200-3436400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:3411200-3436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:3411400-3425600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:3411800-3420000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:3412400-3417600	Weak transcription	NHEK	skin
16	chr4:3412600-3417800	Weak transcription	Fetal Brain Female	brain
17	chr4:3413200-3417800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:3413200-3420000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:3413600-3418600	Weak transcription	Thymus	Thymus
20	chr4:3413600-3437000	Strong transcription	Esophagus	oesophagus
21	chr4:3414000-3418000	Weak transcription	HUVEC	blood vessel
22	chr4:3414400-3418800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:3414400-3419600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:3414600-3417600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr4:3415000-3435600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:3415000-3436400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:3415200-3417600	Enhancers	Ovary	ovary
28	chr4:3415400-3437000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:3415600-3426000	Strong transcription	HepG2	liver
30	chr4:3415600-3433600	Weak transcription	Fetal Kidney	kidney
31	chr4:3415800-3417600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:3415800-3417600	Weak transcription	NHLF	lung
33	chr4:3415800-3417800	Weak transcription	Primary T cells from cord blood	blood
34	chr4:3415800-3418000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr4:3415800-3418600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:3415800-3418800	Genic enhancers	Fetal Muscle Leg	muscle
37	chr4:3415800-3419600	Weak transcription	Fetal Heart	heart
38	chr4:3415800-3421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:3415800-3436400	Strong transcription	Lung	lung
40	chr4:3416000-3417600	Enhancers	Adipose Nuclei	Adipose
41	chr4:3416000-3417600	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:3416000-3420600	Strong transcription	Right Ventricle	heart
43	chr4:3416200-3417800	Weak transcription	Brain Substantia Nigra	brain
44	chr4:3416200-3417800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr4:3416200-3417800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:3416200-3418600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:3416200-3419400	Strong transcription	Liver	Liver
48	chr4:3416200-3419600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:3416200-3419600	Strong transcription	Brain Germinal Matrix	brain
50	chr4:3416200-3423000	Strong transcription	Fetal Stomach	stomach

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