Variant report

Variant	rs419096
Chromosome Location	chr4:2793155-2793156
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	CTCF	chr4:2793151-2793205	GM12891	blood:	n/a	n/a
2	ELF1	chr4:2793084-2793497	HepG2	liver:	n/a	chr4:2793337-2793348 chr4:2793336-2793349
3	MXI1	chr4:2792579-2794034	HepG2	liver:	n/a	chr4:2793532-2793541
4	POLR2A	chr4:2793033-2793647	HepG2	liver:	n/a	n/a
5	MAX	chr4:2792479-2794953	HepG2	liver:	n/a	chr4:2794661-2794670 chr4:2794620-2794630 chr4:2793915-2793924 chr4:2794622-2794629 chr4:2794621-2794630
6	POLR2A	chr4:2793149-2793398	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:56708745..56710384-chr4:2792772..2795707,2	MCF-7	breast:
2	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
3	chr4:2747762..2749631-chr4:2792951..2795246,2	MCF-7	breast:
4	chr4:2753714..2768807-chr4:2789818..2806638,47	MCF-7	breast:
5	chr4:2757714..2759449-chr4:2793017..2796252,4	K562	blood:
6	chr4:2745843..2747557-chr4:2792852..2794917,2	MCF-7	breast:

Variant related genes	Relation type
SH3BP2	TF binding region
ENSG00000109736	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10011310	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13113803	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13137906	0.83[ASN][1000 genomes]
rs172998	0.82[ASN][1000 genomes]
rs1784148	0.83[ASN][1000 genomes]
rs1784149	0.83[ASN][1000 genomes]
rs182820	0.80[ASN][1000 genomes]
rs190160	0.83[ASN][1000 genomes]
rs2269485	0.83[ASN][1000 genomes]
rs2282770	0.83[ASN][1000 genomes]
rs2282771	0.83[ASN][1000 genomes]
rs231334	0.83[ASN][1000 genomes]
rs3213501	0.84[ASN][1000 genomes]
rs34993433	0.84[ASN][1000 genomes]
rs370470	0.88[ASN][1000 genomes]
rs385715	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs390288	0.83[ASN][1000 genomes]
rs393635	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs397292	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402855	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs407770	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408102	0.86[ASN][1000 genomes]
rs421714	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs422734	0.90[ASN][1000 genomes]
rs426904	0.90[ASN][1000 genomes]
rs433030	0.89[ASN][1000 genomes]
rs445160	0.90[ASN][1000 genomes]
rs450080	0.90[ASN][1000 genomes]
rs6820967	0.89[ASN][1000 genomes]
rs9685721	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2786600-2794800	Enhancers	Primary B cells from cord blood	blood
2	chr4:2786800-2794800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr4:2786800-2794800	Enhancers	Primary B cells from peripheral blood	blood
4	chr4:2787400-2794800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:2787800-2794400	Enhancers	Spleen	Spleen
6	chr4:2787800-2794800	Enhancers	Fetal Muscle Leg	muscle
7	chr4:2788000-2794200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:2788200-2793600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:2789800-2793400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:2789800-2793400	Weak transcription	Pancreas	Pancrea
11	chr4:2789800-2793400	Weak transcription	Stomach Mucosa	stomach
12	chr4:2789800-2793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:2789800-2793800	Weak transcription	A549	lung
14	chr4:2789800-2794800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr4:2789800-2794800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:2790000-2793800	Weak transcription	Gastric	stomach
17	chr4:2790000-2794000	Weak transcription	Hela-S3	cervix
18	chr4:2790000-2794400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr4:2790000-2794800	Weak transcription	Brain Substantia Nigra	brain
20	chr4:2790200-2793400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:2790200-2795400	Weak transcription	Fetal Lung	lung
22	chr4:2790400-2793800	Weak transcription	Lung	lung
23	chr4:2790400-2794000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:2790400-2794400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:2790400-2794400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:2790400-2794600	Weak transcription	Thymus	Thymus
27	chr4:2790600-2793200	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:2790600-2793200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:2790600-2793400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:2790600-2794800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:2790600-2795000	Weak transcription	HSMMtube	muscle
32	chr4:2790600-2795200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:2790800-2793400	Weak transcription	Left Ventricle	heart
34	chr4:2790800-2793600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:2790800-2793800	Weak transcription	Right Atrium	heart
36	chr4:2790800-2794000	Weak transcription	Brain Anterior Caudate	brain
37	chr4:2790800-2794000	Weak transcription	Fetal Heart	heart
38	chr4:2790800-2794200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr4:2790800-2794400	Weak transcription	Primary T cells from cord blood	blood
40	chr4:2790800-2794400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr4:2790800-2794400	Weak transcription	Brain Germinal Matrix	brain
42	chr4:2790800-2794800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:2790800-2794800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:2790800-2794800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:2791000-2793400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:2791000-2795000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:2791200-2793600	Weak transcription	Fetal Intestine Large	intestine
48	chr4:2791200-2794200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr4:2791400-2794000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr4:2791400-2795200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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