Variant report

Variant	rs9996929
Chromosome Location	chr4:2798812-2798813
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	MAX	chr4:2797749-2798911	A549	lung:	n/a	chr4:2797976-2797992 chr4:2797985-2797995 chr4:2797983-2797998 chr4:2797984-2797995 chr4:2798587-2798597 chr4:2797984-2797995 chr4:2797985-2797994
2	MAX	chr4:2798230-2798900	MCF-7	breast:	n/a	chr4:2798587-2798597
3	MAX	chr4:2797785-2798817	A549	lung:	n/a	chr4:2797976-2797992 chr4:2797985-2797995 chr4:2797983-2797998 chr4:2797984-2797995 chr4:2798587-2798597 chr4:2797984-2797995 chr4:2797985-2797994
4	TFAP2C	chr4:2797794-2798856	Hela-S3	cervix:	n/a	chr4:2798314-2798329 chr4:2798294-2798309
5	MAX	chr4:2798053-2798823	MCF-7	breast:	n/a	chr4:2798587-2798597
6	TCF12	chr4:2797780-2798916	MCF-7	breast:	n/a	chr4:2798881-2798891
7	POLR2A	chr4:2798236-2798851	Hela-S3	cervix:	n/a	n/a
8	E2F6	chr4:2798194-2798839	A549	lung:	n/a	n/a

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	chr4:2764307..2766029-chr4:2796007..2799885,3	MCF-7	breast:
4	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
5	chr4:2798466..2800490-chr4:2934363..2936581,2	K562	blood:
6	chr4:2794525..2804465-chr4:2841103..2847851,19	MCF-7	breast:
7	chr4:2798106..2801583-chr4:2843513..2845994,4	MCF-7	breast:
8	chr4:2798786..2800390-chr4:3294087..3295620,2	MCF-7	breast:
9	chr4:2798213..2801828-chr4:2930948..2933812,4	MCF-7	breast:
10	chr4:2754950..2759334-chr4:2798371..2803453,5	MCF-7	breast:
11	chr4:2798770..2801758-chr4:2941180..2943976,2	K562	blood:
12	chr4:2797605..2799131-chr4:3074789..3077208,2	MCF-7	breast:
13	chr4:2753714..2768807-chr4:2789818..2806638,47	MCF-7	breast:
14	chr4:2794820..2799191-chr4:2824314..2827597,4	MCF-7	breast:
15	chr4:2793845..2803067-chr4:2816443..2823671,22	MCF-7	breast:

Variant related genes	Relation type
SH3BP2	TF binding region
ENSG00000087266	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000159788	Chromatin interaction
ENSG00000109736	Chromatin interaction
ENSG00000251075	Chromatin interaction
ENSG00000197386	Chromatin interaction
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs28656878	1.00[AFR][1000 genomes]
rs9994090	1.00[AFR][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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2795400-2801400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:2795600-2799000	Flanking Active TSS	Hela-S3	cervix
3	chr4:2795800-2799000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:2795800-2799000	Enhancers	Small Intestine	intestine
5	chr4:2795800-2799200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr4:2795800-2803000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:2796000-2799800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr4:2796000-2802400	Enhancers	Brain Germinal Matrix	brain
9	chr4:2796000-2803400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr4:2796000-2803600	Enhancers	Fetal Brain Male	brain
11	chr4:2796000-2803800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:2796200-2799000	Genic enhancers	Fetal Intestine Small	intestine
13	chr4:2796200-2799800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr4:2796200-2799800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:2796200-2800000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr4:2796200-2802000	Enhancers	Fetal Muscle Trunk	muscle
17	chr4:2796200-2802400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:2796200-2803400	Enhancers	Pancreas	Pancrea
19	chr4:2796200-2803400	Enhancers	Right Atrium	heart
20	chr4:2796200-2803600	Enhancers	Fetal Brain Female	brain
21	chr4:2796200-2813800	Enhancers	Left Ventricle	heart
22	chr4:2796400-2799200	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr4:2796400-2799400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:2796400-2799600	Enhancers	Primary hematopoietic stem cells	blood
25	chr4:2796400-2800600	Enhancers	Gastric	stomach
26	chr4:2796600-2803600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:2796600-2814600	Enhancers	Stomach Mucosa	stomach
28	chr4:2796800-2799000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:2796800-2799200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:2796800-2799400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr4:2796800-2800000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:2796800-2800000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:2796800-2800000	Enhancers	Brain Hippocampus Middle	brain
34	chr4:2796800-2800000	Genic enhancers	Fetal Stomach	stomach
35	chr4:2796800-2800400	Enhancers	Brain Anterior Caudate	brain
36	chr4:2796800-2801200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:2796800-2802200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr4:2796800-2803600	Enhancers	NHDF-Ad	bronchial
39	chr4:2796800-2803800	Enhancers	HUVEC	blood vessel
40	chr4:2797000-2799200	Weak transcription	Thymus	Thymus
41	chr4:2797000-2799400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:2797000-2800000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:2797000-2800000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr4:2797000-2800400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr4:2797000-2800400	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr4:2797000-2800400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr4:2797000-2801200	Enhancers	Fetal Thymus	thymus
48	chr4:2797000-2802000	Weak transcription	Ovary	ovary
49	chr4:2797000-2803800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr4:2797200-2799000	Weak transcription	GM12878-XiMat	blood

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