Variant report

Variant	rs28660254
Chromosome Location	chr4:3115577-3115578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:3074016..3078502-chr4:3111809..3117809,7	MCF-7	breast:
2	chr4:3108607..3111576-chr4:3111924..3115873,4	MCF-7	breast:
3	chr4:3113077..3115750-chr4:3467353..3469747,2	MCF-7	breast:
4	chr4:3112475..3121644-chr4:3122211..3126506,10	MCF-7	breast:
5	chr4:3106351..3108490-chr4:3114855..3116846,2	MCF-7	breast:
6	chr4:3111872..3117206-chr4:3129314..3133133,7	MCF-7	breast:
7	chr4:3075012..3079488-chr4:3111729..3116028,6	MCF-7	breast:
8	chr4:3108596..3110379-chr4:3112346..3116556,3	K562	blood:
9	chr4:3110927..3117533-chr4:3461507..3465762,15	MCF-7	breast:
10	chr4:3046626..3049120-chr4:3114672..3116966,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197386	Chromatin interaction
ENSG00000251075	Chromatin interaction
ENSG00000175920	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10000252	0.86[EUR][1000 genomes]
rs10002065	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006129	0.84[EUR][1000 genomes]
rs10006977	0.87[EUR][1000 genomes]
rs10009229	1.00[EUR][1000 genomes]
rs10009935	0.84[EUR][1000 genomes]
rs10011127	1.00[EUR][1000 genomes]
rs10014333	0.87[EUR][1000 genomes]
rs10016755	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10030079	0.86[EUR][1000 genomes]
rs10034313	0.93[EUR][1000 genomes]
rs10222986	0.87[EUR][1000 genomes]
rs1419036	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843857	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843866	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843869	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843871	0.92[AFR][1000 genomes]
rs28387056	0.93[EUR][1000 genomes]
rs28393280	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28394705	0.84[EUR][1000 genomes]
rs28468636	0.80[EUR][1000 genomes]
rs28485764	0.84[EUR][1000 genomes]
rs28580164	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28583447	0.80[EUR][1000 genomes]
rs28583552	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28584232	0.84[EUR][1000 genomes]
rs28629394	0.84[EUR][1000 genomes]
rs28634516	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28652828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28670335	0.93[EUR][1000 genomes]
rs28696693	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28714390	0.84[EUR][1000 genomes]
rs28718346	0.87[EUR][1000 genomes]
rs28755900	0.90[EUR][1000 genomes]
rs3025836	0.93[EUR][1000 genomes]
rs363138	0.93[EUR][1000 genomes]
rs4346595	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56021098	0.92[AFR][1000 genomes]
rs56148664	0.93[AFR][1000 genomes]
rs57792935	0.93[AFR][1000 genomes]
rs57875258	0.92[AFR][1000 genomes]
rs6830019	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6835897	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6836289	0.93[AFR][1000 genomes]
rs7436457	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7664480	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7693317	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994689	0.93[EUR][1000 genomes]
rs9995782	0.93[EUR][1000 genomes]
rs9996075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3080000-3117800	Weak transcription	Small Intestine	intestine
2	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr4:3094400-3123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:3097200-3143400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:3100000-3159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:3101000-3120600	Strong transcription	Fetal Stomach	stomach
10	chr4:3101000-3122600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr4:3101000-3124200	Strong transcription	Fetal Intestine Large	intestine
12	chr4:3101000-3124400	Strong transcription	Thymus	Thymus
13	chr4:3101600-3124200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:3105400-3123800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr4:3105400-3124800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:3105800-3121400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:3106400-3123400	Strong transcription	Primary T cells from cord blood	blood
18	chr4:3106400-3123800	Strong transcription	Fetal Thymus	thymus
19	chr4:3106400-3145000	Strong transcription	Dnd41	blood
20	chr4:3106600-3115600	Strong transcription	Fetal Brain Female	brain
21	chr4:3106800-3125200	Strong transcription	Primary B cells from cord blood	blood
22	chr4:3108400-3119600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:3108400-3123000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:3108600-3125800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr4:3108600-3136600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:3108600-3163000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:3108800-3115800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:3108800-3120600	Strong transcription	Fetal Intestine Small	intestine
29	chr4:3108800-3123600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:3108800-3164600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:3109000-3123200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:3109000-3123600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:3109000-3124200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:3109200-3119600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr4:3109200-3123200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:3109200-3142600	Strong transcription	GM12878-XiMat	blood
37	chr4:3109400-3124600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr4:3109400-3130400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr4:3109800-3115600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:3109800-3116400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:3109800-3117000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr4:3109800-3120400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr4:3110000-3116200	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:3110000-3117200	Weak transcription	Colonic Mucosa	Colon
45	chr4:3110000-3117200	Weak transcription	Fetal Brain Male	brain
46	chr4:3110400-3116200	Weak transcription	Fetal Kidney	kidney
47	chr4:3110400-3116600	Weak transcription	Spleen	Spleen
48	chr4:3110400-3117600	Weak transcription	K562	blood
49	chr4:3110400-3123400	Weak transcription	Stomach Mucosa	stomach
50	chr4:3110600-3123400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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