Variant report

Variant	rs4948109
Chromosome Location	chr7:56243607-56243608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUMF2-9	chr7:56243327-56244105	NONHSAT120737

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10281780	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764929	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231115	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784297	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804108	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816244	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
5	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv526294	chr7:56171489-56622630	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
11	nsv1016771	chr7:56174828-56643856	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv538862	chr7:56174828-56643856	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv1015254	chr7:56190072-56334445	Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1034763	chr7:56190072-56336627	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1026887	chr7:56191763-56330473	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv3368661	chr7:56201127-56591279	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv5756	chr7:56203664-56246844	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv508455	chr7:56212547-56257101	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv3417738	chr7:56241108-56244206	Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv971171	chr7:56243262-56368822	Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56242000-56243800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:56242200-56244000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:56242400-56243800	Active TSS	Aorta	Aorta
4	chr7:56242400-56243800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
5	chr7:56242400-56243800	ZNF genes & repeats	Spleen	Spleen
6	chr7:56242400-56244000	Active TSS	Colon Smooth Muscle	Colon
7	chr7:56242400-56244000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
8	chr7:56242600-56243800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
9	chr7:56242600-56243800	Active TSS	Brain Substantia Nigra	brain
10	chr7:56242600-56243800	ZNF genes & repeats	Colonic Mucosa	Colon
11	chr7:56242600-56243800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
12	chr7:56242600-56243800	Bivalent/Poised TSS	Fetal Stomach	stomach
13	chr7:56242600-56243800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr7:56242600-56243800	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
15	chr7:56242800-56244000	Active TSS	Ovary	ovary
16	chr7:56242800-56244000	Active TSS	Psoas Muscle	Psoas
17	chr7:56243000-56243800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
18	chr7:56243200-56243800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:56243200-56243800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:56243200-56243800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
21	chr7:56243200-56243800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:56243200-56243800	Flanking Bivalent TSS/Enh	Placenta	Placenta
23	chr7:56243400-56243800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
24	chr7:56243400-56243800	Enhancers	Right Atrium	heart
25	chr7:56243400-56243800	Bivalent/Poised TSS	Right Ventricle	heart
26	chr7:56243400-56244000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr7:56243400-56244000	Enhancers	Gastric	stomach
28	chr7:56243600-56243800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
29	chr7:56243600-56243800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
30	chr7:56243600-56243800	Bivalent/Poised TSS	Fetal Kidney	kidney
31	chr7:56243600-56243800	Active TSS	Pancreas	Pancrea
32	chr7:56243600-56243800	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr7:56243600-56244000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr7:56243600-56244000	Bivalent Enhancer	Fetal Muscle Leg	muscle

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