Variant report

Variant	rs363091
Chromosome Location	chr4:3202138-3202139
allele	C/T
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	chr4:3201796-3202229	SK-N-MC	brain:	n/a	n/a
2	E2F4	chr4:3202107-3202222	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:3196534..3198445-chr4:3199145..3202681,3	MCF-7	breast:
2	chr4:3200457..3202229-chr4:3205409..3207674,2	K562	blood:
3	chr4:3201399..3203934-chr4:3207301..3210126,2	MCF-7	breast:

Variant related genes	Relation type
HTT	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10006373	1.00[EUR][1000 genomes]
rs10012793	0.87[EUR][1000 genomes]
rs10021254	1.00[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs10034669	0.93[EUR][1000 genomes]
rs10155264	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10488840	0.93[EUR][1000 genomes]
rs110501	0.83[LWK][hapmap];0.84[MKK][hapmap]
rs16844026	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs16844028	0.93[EUR][1000 genomes]
rs2003530	0.91[EUR][1000 genomes]
rs2005787	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2071655	1.00[LWK][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap]
rs2071662	0.81[AFR][1000 genomes]
rs2071704	0.81[MKK][hapmap]
rs2285086	1.00[LWK][hapmap];0.92[YRI][hapmap]
rs2298971	0.88[AFR][1000 genomes]
rs28436280	0.99[EUR][1000 genomes]
rs28643391	0.92[EUR][1000 genomes]
rs3025825	0.92[EUR][1000 genomes]
rs3025849	1.00[ASN][1000 genomes]
rs3025851	1.00[ASN][1000 genomes]
rs3095076	1.00[ASN][1000 genomes]
rs362274	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs362276	0.97[EUR][1000 genomes]
rs362277	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs362278	0.93[EUR][1000 genomes]
rs362303	0.85[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs362304	0.81[EUR][1000 genomes]
rs362310	1.00[CEU][hapmap]
rs362323	0.92[EUR][1000 genomes]
rs362325	0.84[CEU][hapmap]
rs362331	0.98[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs362338	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs363067	1.00[CHD][hapmap]
rs363070	1.00[CHD][hapmap]
rs363074	1.00[ASN][1000 genomes]
rs363082	1.00[CHD][hapmap]
rs363090	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363093	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs363094	0.91[EUR][1000 genomes]
rs363095	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs363097	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs363098	0.93[EUR][1000 genomes]
rs363100	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs363101	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363102	1.00[ASN][1000 genomes]
rs363104	1.00[ASN][1000 genomes]
rs363106	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs363124	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363125	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363128	0.93[EUR][1000 genomes]
rs363141	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4690072	0.93[YRI][hapmap]
rs4690073	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs59147561	0.80[EUR][1000 genomes]
rs61792513	1.00[ASN][1000 genomes]
rs61792535	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446723	0.93[YRI][hapmap]
rs6446724	0.93[EUR][1000 genomes]
rs6446725	0.93[EUR][1000 genomes]
rs6828615	0.95[EUR][1000 genomes]
rs6828882	0.92[EUR][1000 genomes]
rs6829069	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6834455	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[EUR][1000 genomes]
rs6835567	0.99[EUR][1000 genomes]
rs6839081	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839274	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs6843895	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[EUR][1000 genomes]
rs6844859	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs7438553	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7654034	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7665816	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]
rs7667354	0.93[EUR][1000 genomes]
rs7683309	0.93[EUR][1000 genomes]
rs7688390	0.91[EUR][1000 genomes]
rs7691627	0.98[LWK][hapmap];0.93[YRI][hapmap]
rs7692292	1.00[ASN][1000 genomes]
rs82333	0.83[LWK][hapmap];0.84[MKK][hapmap]
rs916171	0.98[LWK][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs9993542	1.00[CHD][hapmap]
rs9993781	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs363091	SH3BP2	cis	cerebellum	SCAN
rs363091	OTOP1	cis	cerebellum	SCAN
rs363091	JAKMIP1	cis	cerebellum	SCAN
rs363091	TMEM129	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3167800-3203400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr4:3168000-3202800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:3168000-3203000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
7	chr4:3172000-3202800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:3172800-3202800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr4:3174000-3204000	Strong transcription	Stomach Smooth Muscle	stomach
11	chr4:3181600-3206600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:3182400-3203200	Strong transcription	Fetal Intestine Large	intestine
13	chr4:3183000-3202600	Strong transcription	Liver	Liver
14	chr4:3183400-3206800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:3185200-3208400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:3190600-3203600	Weak transcription	Small Intestine	intestine
17	chr4:3191200-3203400	Weak transcription	Fetal Heart	heart
18	chr4:3191200-3208600	Weak transcription	A549	lung
19	chr4:3191600-3203600	Weak transcription	K562	blood
20	chr4:3191800-3207800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:3191800-3208200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:3191800-3211600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:3192800-3208600	Weak transcription	HUVEC	blood vessel
24	chr4:3193600-3204600	Weak transcription	Fetal Kidney	kidney
25	chr4:3193800-3203200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:3193800-3206800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:3193800-3233000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:3194000-3202600	Strong transcription	Gastric	stomach
29	chr4:3194000-3202600	Strong transcription	Lung	lung
30	chr4:3194000-3203600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:3194000-3206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:3194000-3237600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:3194200-3203200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:3194200-3210600	Weak transcription	HMEC	breast
35	chr4:3194200-3212600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:3194400-3203000	Strong transcription	GM12878-XiMat	blood
37	chr4:3194600-3203000	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:3196000-3202800	Strong transcription	Placenta	Placenta
39	chr4:3196000-3203200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:3196000-3203600	Strong transcription	Fetal Stomach	stomach
41	chr4:3196000-3204000	Strong transcription	Aorta	Aorta
42	chr4:3196000-3242600	Strong transcription	Fetal Intestine Small	intestine
43	chr4:3196800-3202600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:3196800-3202800	Strong transcription	Osteobl	bone
45	chr4:3197000-3202600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:3197200-3203000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:3197200-3203800	Weak transcription	Fetal Brain Male	brain
48	chr4:3197400-3202800	Strong transcription	Colonic Mucosa	Colon
49	chr4:3197400-3203000	Strong transcription	Fetal Brain Female	brain
50	chr4:3198600-3202800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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