Variant report

Variant	rs2836823
Chromosome Location	chr21:40380249-40380250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40379466..40381307-chr21:40382191..40384839,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237721	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2836815	0.82[JPT][hapmap]
rs2836822	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3746882	1.00[LWK][hapmap]
rs9305658	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9305659	0.82[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Nicotine dependence	17158188	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2836823	RIPK4	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40366400-40381600	Weak transcription	Psoas Muscle	Psoas
2	chr21:40372000-40385000	Weak transcription	Pancreas	Pancrea
3	chr21:40374000-40380400	Enhancers	Adipose Nuclei	Adipose
4	chr21:40374600-40380400	Enhancers	Fetal Muscle Leg	muscle
5	chr21:40374800-40381000	Enhancers	Fetal Thymus	thymus
6	chr21:40375800-40380400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr21:40376000-40381200	Enhancers	Fetal Muscle Trunk	muscle
8	chr21:40376000-40381200	Enhancers	Placenta	Placenta
9	chr21:40376000-40384600	Enhancers	Lung	lung
10	chr21:40376600-40380400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr21:40376600-40383200	Enhancers	Fetal Lung	lung
12	chr21:40376800-40380400	Enhancers	Colonic Mucosa	Colon
13	chr21:40377400-40380600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr21:40377400-40381600	Weak transcription	Aorta	Aorta
15	chr21:40377600-40382400	Weak transcription	Fetal Intestine Large	intestine
16	chr21:40377600-40384200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr21:40377600-40384600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr21:40377800-40383000	Weak transcription	Thymus	Thymus
19	chr21:40378400-40381800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr21:40378400-40382600	Weak transcription	Right Ventricle	heart
21	chr21:40378400-40383200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr21:40378400-40385000	Weak transcription	Esophagus	oesophagus
23	chr21:40378600-40394600	Weak transcription	Gastric	stomach
24	chr21:40378800-40383000	Weak transcription	Dnd41	blood
25	chr21:40379000-40380600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr21:40379200-40380600	Weak transcription	Brain Hippocampus Middle	brain
27	chr21:40379200-40381200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr21:40379200-40381600	Weak transcription	Left Ventricle	heart
29	chr21:40379200-40382400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr21:40379200-40382600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr21:40379200-40385000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr21:40379200-40386000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr21:40379200-40392600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr21:40379400-40380600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr21:40379400-40380600	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr21:40379400-40381000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr21:40379400-40382600	Weak transcription	Primary B cells from cord blood	blood
38	chr21:40379600-40380600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr21:40379600-40381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr21:40379600-40382800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr21:40379800-40381600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr21:40379800-40382600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr21:40379800-40383200	Enhancers	HepG2	liver
44	chr21:40380000-40380400	Enhancers	Primary hematopoietic stem cells	blood
45	chr21:40380000-40380400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr21:40380000-40380400	Enhancers	Stomach Smooth Muscle	stomach
47	chr21:40380000-40380400	Enhancers	Spleen	Spleen
48	chr21:40380000-40382200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr21:40380000-40382400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr21:40380000-40386200	Weak transcription	Rectal Mucosa Donor 31	rectum

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