Variant report

Variant	rs16841504
Chromosome Location	chr4:7968888-7968889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7966853..7969531-chr4:7971692..7973616,2	MCF-7	breast:
2	chr20:52208463..52210138-chr4:7967818..7969882,2	MCF-7	breast:
3	chr4:7968293..7969808-chr4:7972289..7974865,2	MCF-7	breast:
4	chr4:7938506..7945813-chr4:7968503..7977501,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13137347	0.93[ASN][1000 genomes]
rs2292735	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292736	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292737	0.84[ASN][1000 genomes]
rs2292738	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409515	0.92[ASN][1000 genomes]
rs3749597	0.86[ASN][1000 genomes]
rs4696709	0.85[ASN][1000 genomes]
rs4696886	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62290613	0.81[ASN][1000 genomes]
rs9799872	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv593621	chr4:7943106-7969594	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv829851	chr4:7958698-8049060	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7959400-7971600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:7963000-7971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7963200-7969200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:7963200-7969200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:7963200-7969400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:7963200-7969800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:7963200-7971600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:7963200-7971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:7963400-7975400	Weak transcription	Aorta	Aorta
10	chr4:7963600-7969400	Weak transcription	Fetal Kidney	kidney
11	chr4:7963800-7969200	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:7963800-7969400	Weak transcription	Osteobl	bone
13	chr4:7964400-7971600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr4:7964800-7971000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:7965000-7969400	Weak transcription	Gastric	stomach
16	chr4:7965400-7969600	Weak transcription	GM12878-XiMat	blood
17	chr4:7965600-7969400	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:7965600-7971200	Weak transcription	Brain Anterior Caudate	brain
19	chr4:7965800-7969600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:7966000-7971600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:7966400-7970400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
22	chr4:7967000-7969600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:7967000-7969600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:7967000-7987600	Weak transcription	Psoas Muscle	Psoas
25	chr4:7967200-7969000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:7967200-7969800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:7967200-7969800	Weak transcription	Fetal Intestine Small	intestine
28	chr4:7967200-7971000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:7967200-7971000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:7967400-7969200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:7967400-7969200	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:7967400-7969200	Weak transcription	HUVEC	blood vessel
33	chr4:7967400-7969400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:7967400-7969600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:7967400-7970000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:7967600-7969000	Weak transcription	Colonic Mucosa	Colon
37	chr4:7967600-7969200	Weak transcription	Right Ventricle	heart
38	chr4:7967600-7969200	Weak transcription	Stomach Mucosa	stomach
39	chr4:7967600-7969400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:7967600-7969400	Weak transcription	Adipose Nuclei	Adipose
41	chr4:7967600-7969400	Weak transcription	Fetal Stomach	stomach
42	chr4:7967600-7969400	Weak transcription	Left Ventricle	heart
43	chr4:7967600-7969400	Weak transcription	Lung	lung
44	chr4:7967600-7969600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:7967600-7969800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr4:7967800-7969000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:7967800-7969200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr4:7967800-7969200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:7967800-7969200	Weak transcription	Fetal Thymus	thymus
50	chr4:7967800-7969600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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