Variant report

Variant	rs323861
Chromosome Location	chr3:52025816-52025817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52024177..52026673-chr3:52066443..52068410,2	K562	blood:
2	chr3:52024713..52026364-chr3:52074077..52075668,2	MCF-7	breast:
3	chr3:51974147..51980389-chr3:52024451..52030996,12	K562	blood:
4	chr3:52006271..52012102-chr3:52024917..52032079,14	MCF-7	breast:
5	chr3:51977650..51979400-chr3:52023548..52026271,2	MCF-7	breast:
6	chr3:51974624..51978885-chr3:52015984..52028227,23	K562	blood:

Variant related genes	Relation type
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000272762	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000114786	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11916396	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2015691	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323858	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323859	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs323862	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323865	1.00[ASN][1000 genomes]
rs323866	1.00[ASN][1000 genomes]
rs323867	1.00[ASN][1000 genomes]
rs323868	0.90[AMR][1000 genomes]
rs323879	0.90[AMR][1000 genomes]
rs323890	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323894	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs323897	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs379462	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs380788	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs403620	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs404527	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	0.90[AFR][1000 genomes]
rs433823	1.00[ASN][1000 genomes]
rs451154	0.89[AMR][1000 genomes]
rs72964028	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72964029	1.00[ASN][1000 genomes]
rs7432986	0.81[AFR][1000 genomes]
rs82854	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52017800-52026000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:52017800-52026000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:52017800-52027600	Weak transcription	Fetal Brain Male	brain
4	chr3:52017800-52028200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:52017800-52028200	Weak transcription	Aorta	Aorta
6	chr3:52017800-52028600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:52018000-52026000	Weak transcription	Primary B cells from cord blood	blood
8	chr3:52018000-52026400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:52018000-52028000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:52018200-52026000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:52018200-52026000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr3:52018200-52026200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:52018200-52026200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:52018200-52026200	Weak transcription	HUVEC	blood vessel
15	chr3:52018200-52026400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:52018200-52026600	Weak transcription	Brain Anterior Caudate	brain
17	chr3:52018200-52027400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:52018200-52027600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:52018400-52026000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:52018400-52026000	Weak transcription	Left Ventricle	heart
21	chr3:52018400-52026000	Weak transcription	NHDF-Ad	bronchial
22	chr3:52018400-52026600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:52018400-52026800	Weak transcription	Fetal Kidney	kidney
24	chr3:52018400-52026800	Weak transcription	Psoas Muscle	Psoas
25	chr3:52018400-52028400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:52018400-52028400	Weak transcription	Brain Angular Gyrus	brain
27	chr3:52018600-52026000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:52018600-52026000	Weak transcription	NH-A	brain
29	chr3:52018600-52026200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:52018600-52026200	Weak transcription	Dnd41	blood
31	chr3:52018600-52026600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:52019200-52026800	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:52019800-52026200	Weak transcription	Small Intestine	intestine
34	chr3:52020400-52026000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:52020600-52026000	Weak transcription	Gastric	stomach
36	chr3:52020600-52026800	Weak transcription	Pancreas	Pancrea
37	chr3:52021000-52026200	Weak transcription	Esophagus	oesophagus
38	chr3:52021200-52026200	Weak transcription	Colonic Mucosa	Colon
39	chr3:52021200-52028000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:52021400-52026200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:52021600-52026000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:52022400-52028000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:52022800-52026000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:52022800-52026000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:52022800-52026200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:52023200-52026000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:52023200-52026200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:52023800-52026400	Weak transcription	HSMMtube	muscle
49	chr3:52023800-52028600	Weak transcription	Right Atrium	heart
50	chr3:52024000-52027600	Strong transcription	Fetal Stomach	stomach

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