Variant report

Variant	rs393635
Chromosome Location	chr4:2802113-2802114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2794084..2803742-chr4:2816227..2824357,23	MCF-7	breast:
2	chr4:2795447..2803617-chr4:2934606..2939244,18	MCF-7	breast:
3	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
4	chr4:2801461..2803747-chr4:2835834..2839289,3	MCF-7	breast:
5	chr4:2794525..2804465-chr4:2841103..2847851,19	MCF-7	breast:
6	chr4:2754950..2759334-chr4:2798371..2803453,5	MCF-7	breast:
7	chr4:2753714..2768807-chr4:2789818..2806638,47	MCF-7	breast:
8	chr4:2793845..2803067-chr4:2816443..2823671,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087274	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000109736	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10011310	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13113803	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13137906	0.80[ASN][1000 genomes]
rs1784148	0.80[ASN][1000 genomes]
rs1784149	0.80[ASN][1000 genomes]
rs2269485	0.80[ASN][1000 genomes]
rs2282770	0.80[ASN][1000 genomes]
rs2282771	0.80[ASN][1000 genomes]
rs3213501	0.81[ASN][1000 genomes]
rs34993433	0.81[ASN][1000 genomes]
rs370470	0.85[ASN][1000 genomes]
rs385715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs397292	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs402855	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs407770	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs408102	0.82[ASN][1000 genomes]
rs419096	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs421714	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs422734	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs426904	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs433030	0.86[ASN][1000 genomes]
rs445160	0.87[ASN][1000 genomes]
rs450080	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6820967	0.86[ASN][1000 genomes]
rs9685721	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948659	chr4:1828867-2815632	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1005116	chr4:2633935-2812340	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv470002	chr4:2701098-2836628	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv878445	chr4:2704046-2831383	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv878446	chr4:2710644-2810634	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv878447	chr4:2723531-2831383	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv516797	chr4:2723531-2836628	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv878448	chr4:2723531-2846799	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv878449	chr4:2744480-2831383	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv1002517	chr4:2747905-2822017	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv967941	chr4:2765555-2802771	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv878452	chr4:2789184-2830076	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv461162	chr4:2794320-2846799	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv593436	chr4:2794320-2846799	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2795800-2803000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:2796000-2802400	Enhancers	Brain Germinal Matrix	brain
3	chr4:2796000-2803400	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr4:2796000-2803600	Enhancers	Fetal Brain Male	brain
5	chr4:2796000-2803800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:2796200-2802400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:2796200-2803400	Enhancers	Pancreas	Pancrea
8	chr4:2796200-2803400	Enhancers	Right Atrium	heart
9	chr4:2796200-2803600	Enhancers	Fetal Brain Female	brain
10	chr4:2796200-2813800	Enhancers	Left Ventricle	heart
11	chr4:2796600-2803600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:2796600-2814600	Enhancers	Stomach Mucosa	stomach
13	chr4:2796800-2802200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:2796800-2803600	Enhancers	NHDF-Ad	bronchial
15	chr4:2796800-2803800	Enhancers	HUVEC	blood vessel
16	chr4:2797000-2803800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr4:2797400-2802200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:2797400-2802400	Enhancers	Brain Cingulate Gyrus	brain
19	chr4:2797800-2802400	Enhancers	Brain Substantia Nigra	brain
20	chr4:2798000-2803800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:2798200-2803400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr4:2798400-2809600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:2798600-2803800	Enhancers	Fetal Lung	lung
24	chr4:2798800-2802200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:2798800-2802400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:2798800-2803400	Enhancers	NHEK	skin
27	chr4:2799000-2802800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr4:2799000-2803600	Enhancers	Fetal Heart	heart
29	chr4:2799200-2803400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:2799200-2803800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr4:2799200-2803800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr4:2799400-2802200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:2799400-2802200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:2799400-2802200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:2799400-2802200	Enhancers	Small Intestine	intestine
36	chr4:2799400-2802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:2799400-2803400	Flanking Active TSS	Hela-S3	cervix
38	chr4:2799600-2803600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr4:2799600-2803800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:2799800-2803000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr4:2799800-2803200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr4:2799800-2803400	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr4:2799800-2803400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr4:2799800-2803600	Flanking Active TSS	GM12878-XiMat	blood
45	chr4:2800000-2802200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:2800000-2802600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr4:2800000-2803000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:2800000-2803200	Enhancers	A549	lung
49	chr4:2800000-2803400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr4:2800000-2803400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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