Variant report

Variant	rs3923464
Chromosome Location	chr3:142225388-142225389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142223421..142226102-chr3:142296726..142299495,3	MCF-7	breast:
2	chr3:142221679..142224091-chr3:142224480..142227084,2	K562	blood:
3	chr3:142223658..142226531-chr3:142293631..142295358,2	K562	blood:
4	chr3:142217637..142220232-chr3:142223220..142225683,2	K562	blood:

Variant related genes	Relation type
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10935463	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1129391	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708470	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715514	0.90[EUR][1000 genomes]
rs11718899	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11916455	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923612	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12629001	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12629713	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12634255	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12638158	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12639363	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13063075	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13065800	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13066441	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068397	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13070239	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072346	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13072355	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075259	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13085247	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085261	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089219	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13092234	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13092593	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13093304	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13099184	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2227929	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2227931	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256152	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4558780	0.91[EUR][1000 genomes]
rs4582075	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6440085	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776402	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7432464	0.84[ASN][1000 genomes]
rs7630115	0.84[EUR][1000 genomes]
rs7636909	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641914	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
2	chr3:142200400-142243800	Weak transcription	Fetal Heart	heart
3	chr3:142200600-142271800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:142201000-142239600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:142201000-142240600	Weak transcription	Fetal Brain Male	brain
6	chr3:142201200-142226800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:142201600-142273200	Weak transcription	Esophagus	oesophagus
8	chr3:142201800-142240600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:142201800-142243600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:142201800-142273800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:142202000-142231000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:142202000-142235200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:142202000-142239600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:142202200-142240200	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:142203000-142255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:142203800-142225400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:142203800-142255200	Weak transcription	Gastric	stomach
18	chr3:142204200-142228000	Weak transcription	Pancreas	Pancrea
19	chr3:142204200-142253000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:142204200-142273200	Weak transcription	Spleen	Spleen
21	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
22	chr3:142207400-142238600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:142208200-142226600	Strong transcription	Primary B cells from cord blood	blood
24	chr3:142208400-142231000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:142208800-142239600	Weak transcription	Fetal Brain Female	brain
26	chr3:142209000-142225600	Weak transcription	Brain Angular Gyrus	brain
27	chr3:142209400-142271800	Weak transcription	HepG2	liver
28	chr3:142210400-142231000	Weak transcription	Aorta	Aorta
29	chr3:142210400-142240600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:142211400-142226000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:142211400-142240600	Weak transcription	Brain Germinal Matrix	brain
32	chr3:142212000-142251400	Weak transcription	Brain Anterior Caudate	brain
33	chr3:142212600-142240000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:142212600-142240000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:142212800-142238600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:142213600-142238800	Weak transcription	Ovary	ovary
37	chr3:142216000-142227800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:142217200-142229000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:142217600-142239200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:142217800-142225600	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:142217800-142225800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:142217800-142230600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:142218000-142226200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:142218000-142230800	Weak transcription	Fetal Intestine Large	intestine
45	chr3:142218000-142232400	Weak transcription	Placenta	Placenta
46	chr3:142218200-142230800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:142218200-142232000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:142218200-142251200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:142219200-142227800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:142219800-142226600	Strong transcription	Primary T cells from cord blood	blood

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