Variant report

Variant	rs323901
Chromosome Location	chr3:51973169-51973170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51971377..51973974-chr3:51999528..52003131,3	K562	blood:
2	chr3:51972961..51975805-chr3:51984917..51986970,2	MCF-7	breast:
3	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
4	chr3:51972410..51973936-chr3:52015256..52017849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090097	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000114779	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10433611	1.00[AMR][1000 genomes]
rs1505403	1.00[MEX][hapmap]
rs1587921	1.00[MEX][hapmap]
rs2089225	1.00[AMR][1000 genomes]
rs323875	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs323876	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs323882	1.00[AFR][1000 genomes]
rs323883	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs323888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323889	1.00[MEX][hapmap]
rs323899	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323900	1.00[MEX][hapmap]
rs352646	1.00[AMR][1000 genomes]
rs35898691	1.00[AMR][1000 genomes]
rs380945	1.00[AFR][1000 genomes]
rs386240	1.00[AFR][1000 genomes]
rs433823	1.00[MEX][hapmap]
rs57236484	1.00[AMR][1000 genomes]
rs59196507	1.00[AMR][1000 genomes]
rs61333587	1.00[AMR][1000 genomes]
rs6446153	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs72955239	1.00[AMR][1000 genomes]
rs72955243	1.00[AMR][1000 genomes]
rs72955259	1.00[AMR][1000 genomes]
rs72955260	1.00[AMR][1000 genomes]
rs72955262	1.00[AMR][1000 genomes]
rs72964041	1.00[AMR][1000 genomes]
rs7430706	1.00[AMR][1000 genomes]
rs7612847	1.00[AMR][1000 genomes]
rs973948	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv590280	chr3:51967439-51978327	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51960600-51974400	Weak transcription	Fetal Brain Male	brain
2	chr3:51962600-51973200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:51963800-51974400	Weak transcription	Right Atrium	heart
4	chr3:51964400-51973200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:51964400-51973600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:51964400-51973600	Strong transcription	Thymus	Thymus
7	chr3:51964800-51973600	Strong transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:51965000-51973400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:51965000-51973400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:51965000-51973400	Strong transcription	Brain Cingulate Gyrus	brain
11	chr3:51965000-51973400	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr3:51965000-51973600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:51965000-51973600	Strong transcription	Fetal Muscle Leg	muscle
14	chr3:51965000-51973600	Strong transcription	Fetal Stomach	stomach
15	chr3:51965000-51973600	Strong transcription	Lung	lung
16	chr3:51965200-51973600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr3:51965200-51974200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:51965200-51974600	Strong transcription	Fetal Intestine Small	intestine
19	chr3:51965600-51973400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:51965800-51973200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:51965800-51973200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:51965800-51973400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:51965800-51973400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:51965800-51973600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:51965800-51974000	Strong transcription	NHEK	skin
26	chr3:51965800-51974400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:51966000-51973600	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr3:51966000-51973600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:51966000-51973600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:51966000-51973600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr3:51966000-51973800	Strong transcription	Osteobl	bone
32	chr3:51966000-51974000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:51966000-51974400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:51966400-51973400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr3:51966400-51973400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:51966400-51973600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:51966400-51973600	Strong transcription	Brain Anterior Caudate	brain
38	chr3:51966400-51975000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:51966600-51973200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:51966600-51973400	Strong transcription	Primary T cells from cord blood	blood
41	chr3:51966600-51973400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:51966600-51973400	Strong transcription	Brain Angular Gyrus	brain
43	chr3:51966600-51973400	Strong transcription	Rectal Smooth Muscle	rectum
44	chr3:51966600-51973600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:51966600-51974400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:51966600-51974400	Weak transcription	Stomach Mucosa	stomach
47	chr3:51966800-51973200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:51966800-51973200	Strong transcription	Fetal Lung	lung
49	chr3:51966800-51973400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:51966800-51973400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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