Variant report

Variant	rs16843596
Chromosome Location	chr4:2925576-2925577
allele	G/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	BCL3	chr4:2925231-2925658	GM12878	blood:	n/a	n/a
2	BCL3	chr4:2925239-2925598	GM12878	blood:	n/a	n/a
3	NFATC1	chr4:2925259-2925652	GM12878	blood:	n/a	n/a
4	NFATC1	chr4:2925259-2925639	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2873606..2876373-chr4:2925507..2927684,2	MCF-7	breast:
2	chr4:2794541..2797530-chr4:2924553..2926506,2	K562	blood:
3	chr4:2909857..2911472-chr4:2925477..2927647,2	K562	blood:

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10026792	1.00[CHB][hapmap]
rs1034400	1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10488838	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263331	1.00[ASN][1000 genomes]
rs13061	0.83[AFR][1000 genomes]
rs1574473	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843169	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843451	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843454	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843481	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843500	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843535	1.00[CHB][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843539	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843553	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17833172	1.00[CHB][hapmap]
rs17833250	1.00[CHB][hapmap]
rs1877723	1.00[CHB][hapmap]
rs2005451	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857845	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2858039	1.00[CHB][hapmap]
rs3213502	1.00[CHB][hapmap]
rs34120252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34241425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34550139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585460	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34745961	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34945392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35445752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35508581	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35893718	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35913891	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36038921	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41528047	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690006	1.00[CHB][hapmap]
rs4741	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4969	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56975682	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57155428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57174035	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57557041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57763208	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58059873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58132256	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58196520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58731679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58758786	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58928665	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59426248	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59786983	1.00[ASN][1000 genomes]
rs59790260	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59798370	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60169711	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61117606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61339714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678161	1.00[CHB][hapmap]

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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2893200-2932600	Strong transcription	Fetal Thymus	thymus
2	chr4:2901200-2934600	Weak transcription	Hela-S3	cervix
3	chr4:2907400-2935400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:2910600-2927800	Weak transcription	Small Intestine	intestine
5	chr4:2911200-2935000	Weak transcription	Psoas Muscle	Psoas
6	chr4:2912600-2934800	Weak transcription	A549	lung
7	chr4:2913000-2935000	Weak transcription	K562	blood
8	chr4:2914000-2925800	Weak transcription	NHDF-Ad	bronchial
9	chr4:2915600-2933000	Weak transcription	Right Atrium	heart
10	chr4:2916400-2929800	Weak transcription	Fetal Heart	heart
11	chr4:2917000-2932000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:2917800-2926000	Weak transcription	Aorta	Aorta
13	chr4:2918800-2927800	Weak transcription	Fetal Brain Male	brain
14	chr4:2923400-2925600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr4:2923400-2925600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr4:2923400-2926000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr4:2923400-2932000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr4:2923400-2932000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr4:2923600-2925600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:2923600-2925600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr4:2923600-2925800	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr4:2923800-2925600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:2923800-2926200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr4:2923800-2933600	Strong transcription	Thymus	Thymus
25	chr4:2924000-2925600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr4:2924000-2925600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:2924000-2925600	Strong transcription	Fetal Lung	lung
28	chr4:2924000-2925800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr4:2924000-2925800	Genic enhancers	Lung	lung
30	chr4:2924000-2926000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:2924000-2926200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:2924000-2926200	Genic enhancers	Primary T cells fromperipheralblood	blood
33	chr4:2924000-2926600	Genic enhancers	Brain Hippocampus Middle	brain
34	chr4:2924000-2927000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:2924000-2932000	Strong transcription	Fetal Muscle Leg	muscle
36	chr4:2924000-2934400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:2924200-2925600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:2924200-2925800	Genic enhancers	Primary hematopoietic stem cells	blood
39	chr4:2924200-2926000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:2924200-2926200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:2924200-2926800	Genic enhancers	Brain Cingulate Gyrus	brain
42	chr4:2924200-2927000	Genic enhancers	H1 Cell Line	embryonic stem cell
43	chr4:2924200-2927000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:2924200-2927000	Genic enhancers	Spleen	Spleen
45	chr4:2924200-2927400	Genic enhancers	Fetal Intestine Small	intestine
46	chr4:2924200-2927800	Genic enhancers	Fetal Intestine Large	intestine
47	chr4:2924200-2928200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:2924200-2928800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:2924200-2932000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:2924200-2932400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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