Variant report

Variant	rs7665816
Chromosome Location	chr4:3107604-3107605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3076560..3079556-chr4:3107118..3109310,3	MCF-7	breast:
2	chr4:3073984..3078977-chr4:3107018..3111318,5	MCF-7	breast:
3	chr4:3103289..3106037-chr4:3106708..3108502,2	MCF-7	breast:
4	chr4:3107202..3109277-chr4:3138016..3139789,2	MCF-7	breast:
5	chr4:3106351..3108490-chr4:3114855..3116846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197386	Chromatin interaction
ENSG00000251075	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10006373	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012793	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021254	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs10034669	0.88[EUR][1000 genomes]
rs10155264	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10488840	0.88[EUR][1000 genomes]
rs110501	0.81[LWK][hapmap]
rs16844026	1.00[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs16844028	0.88[EUR][1000 genomes]
rs17780797	0.92[AFR][1000 genomes]
rs2003530	0.86[EUR][1000 genomes]
rs2005787	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071655	0.83[ASW][hapmap];0.98[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2285086	0.83[ASW][hapmap];0.98[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs28436280	0.94[EUR][1000 genomes]
rs28643391	0.90[EUR][1000 genomes]
rs28834148	1.00[ASN][1000 genomes]
rs28867436	0.89[AFR][1000 genomes]
rs3025825	0.87[EUR][1000 genomes]
rs362274	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs362276	0.92[EUR][1000 genomes]
rs362277	0.81[EUR][1000 genomes]
rs362278	0.88[EUR][1000 genomes]
rs362303	0.85[CEU][hapmap]
rs362304	0.81[EUR][1000 genomes]
rs362310	1.00[CEU][hapmap]
rs362323	0.87[EUR][1000 genomes]
rs362325	0.84[CEU][hapmap]
rs362331	0.95[LWK][hapmap];0.85[YRI][hapmap]
rs362338	1.00[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs363063	0.83[AFR][1000 genomes]
rs363067	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363068	1.00[ASN][1000 genomes]
rs363070	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363082	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363090	0.95[EUR][1000 genomes]
rs363091	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.95[EUR][1000 genomes]
rs363093	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363094	0.86[EUR][1000 genomes]
rs363095	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs363097	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363098	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363100	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363101	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs363106	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs363124	0.95[EUR][1000 genomes]
rs363125	0.95[EUR][1000 genomes]
rs363128	0.88[EUR][1000 genomes]
rs363141	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690072	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs4690073	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs59147561	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792464	1.00[ASN][1000 genomes]
rs61792535	0.94[EUR][1000 genomes]
rs6446723	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs6446724	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446725	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828615	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828882	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829069	1.00[CHD][hapmap]
rs6834455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835567	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839081	0.95[EUR][1000 genomes]
rs6839274	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844859	0.85[YRI][hapmap]
rs7438553	0.85[EUR][1000 genomes]
rs7654034	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7663133	1.00[ASN][1000 genomes]
rs7667354	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682324	1.00[ASN][1000 genomes]
rs7683309	0.88[EUR][1000 genomes]
rs7688390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691627	0.83[ASW][hapmap];0.95[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs82333	0.81[LWK][hapmap]
rs916171	0.95[LWK][hapmap];0.89[YRI][hapmap]
rs9993542	1.00[CHD][hapmap]
rs9993781	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak 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	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7665816	SH3BP2	cis	cerebellum	SCAN
rs7665816	OTOP1	cis	cerebellum	SCAN
rs7665816	TMEM129	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3078200-3109800	Weak transcription	Stomach Mucosa	stomach
2	chr4:3078600-3113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:3078800-3108800	Weak transcription	Psoas Muscle	Psoas
4	chr4:3080000-3117800	Weak transcription	Small Intestine	intestine
5	chr4:3084400-3109000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:3084600-3109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:3087800-3108800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr4:3092400-3108200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr4:3093400-3108800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:3093600-3109200	Weak transcription	Fetal Heart	heart
12	chr4:3094400-3123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:3095000-3108200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:3095200-3109000	Weak transcription	A549	lung
15	chr4:3096400-3108000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:3097000-3108200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:3097200-3143400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:3097400-3107800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:3098600-3109800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:3099800-3108200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:3099800-3108200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:3099800-3114400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:3100000-3107800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:3100000-3108000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:3100000-3108200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr4:3100000-3110400	Strong transcription	Primary hematopoietic stem cells	blood
30	chr4:3100000-3159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:3100400-3112000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:3100600-3108000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:3100600-3108400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr4:3100800-3107800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:3100800-3108000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:3101000-3107800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:3101000-3107800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr4:3101000-3108000	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:3101000-3108000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr4:3101000-3108000	Strong transcription	Left Ventricle	heart
41	chr4:3101000-3108200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:3101000-3108200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr4:3101000-3108200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:3101000-3108200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:3101000-3108400	Strong transcription	Fetal Intestine Small	intestine
46	chr4:3101000-3111800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:3101000-3113000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:3101000-3113800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:3101000-3120600	Strong transcription	Fetal Stomach	stomach
50	chr4:3101000-3122600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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