Variant report

Variant	rs324416
Chromosome Location	chr1:46865387-46865388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46862967..46865890-chr1:46874539..46876309,3	K562	blood:
2	chr1:46859776..46861502-chr1:46863907..46865966,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117480	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1887240	0.85[ASN][1000 genomes]
rs324419	0.88[EUR][1000 genomes]
rs3891758	0.88[ASN][1000 genomes]
rs4110477	0.86[ASN][1000 genomes]
rs41294484	0.83[ASN][1000 genomes]
rs45480993	0.91[ASN][1000 genomes]
rs45540335	0.91[ASN][1000 genomes]
rs45564237	1.00[ASN][1000 genomes]
rs45577432	0.97[ASN][1000 genomes]
rs58710660	0.85[ASN][1000 genomes]
rs59082884	0.83[ASN][1000 genomes]
rs60519942	0.85[ASN][1000 genomes]
rs61221162	0.83[ASN][1000 genomes]
rs873978	0.96[ASN][1000 genomes]
rs913168	0.81[ASN][1000 genomes]
rs9865	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46860600-46865800	Weak transcription	Small Intestine	intestine
2	chr1:46860600-46867200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:46861000-46874400	Weak transcription	Primary T cells from cord blood	blood
4	chr1:46861200-46866200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:46861200-46867200	Weak transcription	Lung	lung
6	chr1:46861200-46867200	Weak transcription	Spleen	Spleen
7	chr1:46861200-46872200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:46861200-46879000	Weak transcription	Aorta	Aorta
9	chr1:46861200-46879400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:46861400-46866000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:46861400-46866000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:46861400-46866000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:46861400-46866000	Weak transcription	Fetal Intestine Small	intestine
14	chr1:46861400-46866200	Weak transcription	Thymus	Thymus
15	chr1:46861400-46867200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:46861400-46867200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:46861400-46867400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:46861400-46867400	Weak transcription	Psoas Muscle	Psoas
19	chr1:46861400-46867600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:46861600-46880400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:46861800-46867000	Weak transcription	Esophagus	oesophagus
22	chr1:46862000-46867200	Weak transcription	Adipose Nuclei	Adipose
23	chr1:46862200-46866000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:46862200-46866000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:46862200-46867600	Weak transcription	Left Ventricle	heart
26	chr1:46862200-46867600	Weak transcription	Ovary	ovary
27	chr1:46862400-46867600	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:46862400-46867600	Weak transcription	Fetal Brain Female	brain
29	chr1:46862800-46866000	Weak transcription	Colonic Mucosa	Colon
30	chr1:46863000-46865800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:46863000-46866000	Weak transcription	Fetal Intestine Large	intestine
32	chr1:46863000-46866000	Weak transcription	Pancreas	Pancrea
33	chr1:46863000-46866000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:46863000-46867000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:46863000-46867000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:46863000-46867000	Weak transcription	Liver	Liver
37	chr1:46863000-46867000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:46863000-46867200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:46863000-46867200	Weak transcription	Gastric	stomach
40	chr1:46863000-46867200	Weak transcription	Right Atrium	heart
41	chr1:46863000-46867600	Weak transcription	Fetal Lung	lung
42	chr1:46863200-46865600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:46863200-46867000	Weak transcription	Stomach Mucosa	stomach
44	chr1:46863200-46867000	Weak transcription	NHEK	skin
45	chr1:46864000-46872400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr1:46864600-46865400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr1:46864600-46865400	Enhancers	HSMMtube	muscle
48	chr1:46864600-46867200	Enhancers	Brain Cingulate Gyrus	brain
49	chr1:46864600-46867200	Enhancers	Brain Hippocampus Middle	brain
50	chr1:46864800-46865400	Enhancers	Primary hematopoietic stem cells	blood

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