Variant report

Variant	rs363089
Chromosome Location	chr4:3203578-3203579
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	MYC	chr4:3203568-3204573	NB4	blood:	n/a	n/a
2	POLR2A	chr4:3203430-3205426	GM12891	blood:	n/a	n/a
3	NFATC1	chr4:3203499-3204419	GM12878	blood:	n/a	n/a
4	MAX	chr4:3203511-3204945	NB4	blood:	n/a	n/a
5	BRCA1	chr4:3203534-3203615	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3201399..3203934-chr4:3207301..3210126,2	MCF-7	breast:

Variant related genes	Relation type
HTT	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10021254	1.00[ASN][1000 genomes]
rs10034669	1.00[ASN][1000 genomes]
rs10155264	1.00[ASN][1000 genomes]
rs10488840	1.00[ASN][1000 genomes]
rs1065745	0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843803	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843824	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16844026	1.00[ASN][1000 genomes]
rs16844028	1.00[ASN][1000 genomes]
rs17780617	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003530	1.00[ASN][1000 genomes]
rs28436280	1.00[ASN][1000 genomes]
rs28507598	1.00[ASN][1000 genomes]
rs28643391	1.00[ASN][1000 genomes]
rs3025825	1.00[ASN][1000 genomes]
rs3025849	1.00[EUR][1000 genomes]
rs3025851	1.00[EUR][1000 genomes]
rs34045730	1.00[ASN][1000 genomes]
rs34591077	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362269	1.00[ASN][1000 genomes]
rs362278	1.00[ASN][1000 genomes]
rs362303	1.00[ASN][1000 genomes]
rs362304	1.00[ASN][1000 genomes]
rs362305	1.00[ASN][1000 genomes]
rs362310	1.00[ASN][1000 genomes]
rs362323	1.00[ASN][1000 genomes]
rs362325	1.00[ASN][1000 genomes]
rs363065	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363067	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs363068	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs363069	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363070	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs363071	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363074	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs363078	0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs363082	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs363084	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363087	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363094	1.00[ASN][1000 genomes]
rs363095	1.00[ASN][1000 genomes]
rs363103	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363104	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs363105	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363128	1.00[ASN][1000 genomes]
rs56794194	1.00[ASN][1000 genomes]
rs57196404	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59588638	1.00[ASN][1000 genomes]
rs61460614	1.00[ASN][1000 genomes]
rs61583241	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790489	1.00[ASN][1000 genomes]
rs61790490	1.00[ASN][1000 genomes]
rs61792472	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792477	1.00[ASN][1000 genomes]
rs61792500	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792501	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792502	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792503	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792505	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792507	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792508	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792509	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792510	1.00[ASN][1000 genomes]
rs61792512	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61792515	1.00[ASN][1000 genomes]
rs61792531	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792532	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792533	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829069	0.90[GIH][hapmap]
rs73073018	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7440822	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7674122	1.00[ASN][1000 genomes]
rs7683309	1.00[ASN][1000 genomes]
rs7686771	1.00[ASN][1000 genomes]
rs7692292	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7699037	1.00[ASN][1000 genomes]
rs9993781	1.00[ASN][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

No data

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	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
4	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:3174000-3204000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr4:3181600-3206600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:3183400-3206800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:3185200-3208400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:3190600-3203600	Weak transcription	Small Intestine	intestine
10	chr4:3191200-3208600	Weak transcription	A549	lung
11	chr4:3191600-3203600	Weak transcription	K562	blood
12	chr4:3191800-3207800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:3191800-3208200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:3191800-3211600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:3192800-3208600	Weak transcription	HUVEC	blood vessel
16	chr4:3193600-3204600	Weak transcription	Fetal Kidney	kidney
17	chr4:3193800-3206800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:3193800-3233000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:3194000-3203600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:3194000-3206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:3194000-3237600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:3194200-3210600	Weak transcription	HMEC	breast
23	chr4:3194200-3212600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:3196000-3203600	Strong transcription	Fetal Stomach	stomach
25	chr4:3196000-3204000	Strong transcription	Aorta	Aorta
26	chr4:3196000-3242600	Strong transcription	Fetal Intestine Small	intestine
27	chr4:3197200-3203800	Weak transcription	Fetal Brain Male	brain
28	chr4:3198800-3206200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:3199400-3204200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:3199400-3208600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:3199600-3203600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:3200400-3203800	Genic enhancers	Fetal Muscle Leg	muscle
33	chr4:3200400-3204600	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr4:3201200-3203800	Weak transcription	Right Ventricle	heart
35	chr4:3201200-3206400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:3201400-3204400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:3201400-3204600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:3201400-3205000	Enhancers	Psoas Muscle	Psoas
39	chr4:3201400-3207400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:3201400-3238400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:3201600-3203600	Strong transcription	Primary B cells from cord blood	blood
42	chr4:3201600-3206200	Enhancers	Fetal Lung	lung
43	chr4:3201800-3204000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:3201800-3205000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr4:3202000-3203600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr4:3202000-3203600	Weak transcription	Brain Anterior Caudate	brain
47	chr4:3202000-3203600	Weak transcription	Esophagus	oesophagus
48	chr4:3202000-3203800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr4:3202000-3205600	Enhancers	NHDF-Ad	bronchial
50	chr4:3202200-3203600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links