Variant report

Variant	rs2068230
Chromosome Location	chr3:141623372-141623373
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141594674..141598943-chr3:141621711..141625603,5	MCF-7	breast:
2	chr3:141594460..141597483-chr3:141621419..141624479,3	K562	blood:
3	chr3:141593925..141596999-chr3:141621116..141624479,3	K562	blood:
4	chr3:141622629..141625645-chr3:141628470..141632176,3	K562	blood:

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1072982	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13076111	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1560412	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1560413	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2068229	0.87[CHB][hapmap]
rs2115937	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4441632	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683645	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440043	0.84[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6440044	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6440047	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440050	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767095	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6767302	0.83[EUR][1000 genomes]
rs6773700	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6790923	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7613107	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7622417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639052	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9829502	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859932	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2068230	CLSTN2	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
2	chr3:141597000-141625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:141597200-141625800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:141597800-141627000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:141598000-141625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:141598000-141626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:141598000-141627000	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:141598000-141627200	Weak transcription	Colonic Mucosa	Colon
10	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
11	chr3:141598200-141626000	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:141598200-141627200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:141598200-141640200	Weak transcription	Fetal Brain Male	brain
14	chr3:141598200-141640200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:141598400-141623800	Weak transcription	NH-A	brain
16	chr3:141605200-141627200	Weak transcription	Primary T cells from cord blood	blood
17	chr3:141606200-141623600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:141606800-141625200	Weak transcription	HSMMtube	muscle
19	chr3:141607200-141623800	Weak transcription	HUVEC	blood vessel
20	chr3:141614000-141626000	Weak transcription	Fetal Lung	lung
21	chr3:141614200-141624000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:141614800-141625200	Weak transcription	NHDF-Ad	bronchial
23	chr3:141616200-141623600	Weak transcription	Aorta	Aorta
24	chr3:141616200-141623800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:141616200-141625800	Weak transcription	NHLF	lung
26	chr3:141616200-141627000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:141616200-141646600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr3:141616200-141648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:141616400-141623800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:141616400-141626000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:141616800-141627200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:141618000-141633600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:141618400-141623800	Weak transcription	HSMM	muscle
34	chr3:141619200-141625800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:141619400-141624000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:141619400-141624200	Weak transcription	HMEC	breast
37	chr3:141619400-141625200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:141619400-141625200	Weak transcription	Adipose Nuclei	Adipose
39	chr3:141619400-141625400	Weak transcription	Primary B cells from cord blood	blood
40	chr3:141619400-141625400	Weak transcription	Fetal Brain Female	brain
41	chr3:141619400-141626400	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:141619400-141627200	Weak transcription	Brain Germinal Matrix	brain
43	chr3:141619400-141641600	Weak transcription	Ovary	ovary
44	chr3:141619600-141623800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:141619600-141623800	Weak transcription	Esophagus	oesophagus
46	chr3:141619600-141624000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:141619600-141624000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:141619600-141624000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:141619600-141624000	Weak transcription	A549	lung
50	chr3:141619600-141624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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