Variant report

Variant	rs4679863
Chromosome Location	chr3:159490286-159490287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:159489662-159490389	A549	lung:	n/a	n/a
2	TCF7L2	chr3:159490113-159490300	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159490266..159491970-chr3:159504872..159507711,2	MCF-7	breast:
2	chr3:159481165..159483510-chr3:159489072..159490902,2	K562	blood:

Variant related genes	Relation type
IQCJ-SCHIP1-AS1	TF binding region
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1009058	0.89[CEU][hapmap]
rs10936179	0.94[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107061	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715088	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490735	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491535	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1497762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1675496	0.89[CEU][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap]
rs2010748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169305	0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[ASN][1000 genomes]
rs3851359	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3889309	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3889310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680524	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs56107912	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62270387	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62270397	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6763138	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771478	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6780187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878736	0.81[CEU][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4679863	SMC4	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159483600-159493000	Weak transcription	Gastric	stomach
2	chr3:159483800-159493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:159484000-159494600	Weak transcription	Psoas Muscle	Psoas
4	chr3:159484200-159493200	Weak transcription	Lung	lung
5	chr3:159484200-159501200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:159484400-159493000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:159484400-159493000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:159484400-159493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:159484400-159493200	Weak transcription	Fetal Stomach	stomach
10	chr3:159484400-159505400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:159484600-159500400	Weak transcription	Fetal Intestine Small	intestine
12	chr3:159484800-159493000	Weak transcription	HSMMtube	muscle
13	chr3:159485000-159492600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:159485000-159492800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:159485000-159493000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:159485600-159493000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:159485600-159493000	Weak transcription	HMEC	breast
18	chr3:159485600-159493400	Weak transcription	Fetal Brain Female	brain
19	chr3:159485800-159493000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:159486200-159492200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:159486400-159491000	Weak transcription	HUVEC	blood vessel
22	chr3:159486600-159493200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:159486800-159493000	Weak transcription	Right Ventricle	heart
24	chr3:159486800-159493000	Weak transcription	NH-A	brain
25	chr3:159486800-159493000	Weak transcription	NHEK	skin
26	chr3:159486800-159494000	Weak transcription	Fetal Heart	heart
27	chr3:159487000-159490400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:159487600-159493000	Weak transcription	Right Atrium	heart
29	chr3:159488400-159494600	Weak transcription	Spleen	Spleen
30	chr3:159488600-159490400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:159488600-159491000	Weak transcription	Brain Angular Gyrus	brain
32	chr3:159488600-159492400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:159488600-159492600	Weak transcription	Brain Anterior Caudate	brain
34	chr3:159488600-159492800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:159488600-159493200	Weak transcription	Pancreas	Pancrea
36	chr3:159488600-159493200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:159488800-159492400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:159488800-159492600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:159488800-159492800	Weak transcription	Stomach Mucosa	stomach
40	chr3:159488800-159493000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:159489000-159492800	Weak transcription	NHDF-Ad	bronchial
42	chr3:159489200-159492600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:159489400-159491000	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:159489400-159492400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:159489400-159492400	Weak transcription	NHLF	lung
46	chr3:159489400-159492600	Weak transcription	Osteobl	bone
47	chr3:159489400-159493000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:159489600-159490400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:159489600-159491800	Strong transcription	HSMM	muscle
50	chr3:159489800-159491000	Weak transcription	Rectal Smooth Muscle	rectum

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