Variant report

Variant	rs9815738
Chromosome Location	chr3:88204733-88204734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88197769..88200999-chr3:88203234..88208947,7	MCF-7	breast:
2	chr3:88197032..88201570-chr3:88203720..88209497,8	K562	blood:
3	chr3:88202522..88205546-chr3:88205553..88208457,3	K562	blood:
4	chr3:88105942..88108461-chr3:88204357..88206943,2	K562	blood:
5	chr3:88197168..88201570-chr3:88204371..88207068,4	K562	blood:

Variant related genes	Relation type
ENSG00000229729	Chromatin interaction
ENSG00000179021	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs13067419	0.91[AFR][1000 genomes]
rs3890707	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4241551	0.90[AFR][1000 genomes]
rs4257571	0.94[AFR][1000 genomes]
rs4276211	0.90[AFR][1000 genomes]
rs4276212	0.90[AFR][1000 genomes]
rs4374552	0.94[AFR][1000 genomes]
rs4378991	0.81[AFR][1000 genomes]
rs4384978	0.91[AFR][1000 genomes]
rs4402954	0.86[AFR][1000 genomes]
rs4407422	0.82[AFR][1000 genomes]
rs4414876	0.94[AFR][1000 genomes]
rs4416403	0.82[AFR][1000 genomes]
rs4429658	0.90[AFR][1000 genomes]
rs4432672	0.94[AFR][1000 genomes]
rs4434168	0.90[AFR][1000 genomes]
rs4438681	0.82[AFR][1000 genomes]
rs4485742	0.92[AFR][1000 genomes]
rs4488864	0.91[AFR][1000 genomes]
rs4501136	0.94[AFR][1000 genomes]
rs4507280	0.94[AFR][1000 genomes]
rs4518156	0.94[AFR][1000 genomes]
rs4555548	0.93[AFR][1000 genomes]
rs4568164	0.89[AFR][1000 genomes]
rs4580585	0.93[AFR][1000 genomes]
rs4596173	0.94[AFR][1000 genomes]
rs4616670	0.90[AFR][1000 genomes]
rs4858935	0.80[EUR][1000 genomes]
rs4858936	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4858995	0.90[AFR][1000 genomes]
rs4858997	0.86[AFR][1000 genomes]
rs4859001	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6419866	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6419867	0.81[EUR][1000 genomes]
rs6551268	0.82[AFR][1000 genomes]
rs6551271	0.90[AFR][1000 genomes]
rs6551272	0.90[AFR][1000 genomes]
rs6551274	0.94[AFR][1000 genomes]
rs6551275	0.83[EUR][1000 genomes]
rs6551277	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6551278	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6551279	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6551280	0.82[EUR][1000 genomes]
rs6551282	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6551283	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6551284	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6551285	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6551286	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6551288	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6551289	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6551291	0.88[AFR][1000 genomes]
rs6781333	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6782507	0.94[AFR][1000 genomes]
rs6785359	0.81[EUR][1000 genomes]
rs6786788	0.90[AFR][1000 genomes]
rs6787824	0.91[AFR][1000 genomes]
rs6790629	0.80[AFR][1000 genomes]
rs6791133	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6792208	0.90[AFR][1000 genomes]
rs6793783	0.90[AFR][1000 genomes]
rs6795209	0.89[AFR][1000 genomes]
rs6796355	0.92[AFR][1000 genomes]
rs6799233	0.82[AFR][1000 genomes]
rs6804818	0.90[AFR][1000 genomes]
rs6805804	0.83[AFR][1000 genomes]
rs6805908	0.87[AMR][1000 genomes]
rs7427704	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7429120	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7430158	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7432838	0.82[EUR][1000 genomes]
rs7433285	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7617691	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7618080	0.91[AFR][1000 genomes]
rs7618472	0.82[AFR][1000 genomes]
rs7620130	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7626777	0.90[AFR][1000 genomes]
rs7628689	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7630028	0.91[AFR][1000 genomes]
rs7630240	0.92[AFR][1000 genomes]
rs7632123	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7635996	0.86[AFR][1000 genomes]
rs7637431	0.81[EUR][1000 genomes]
rs7639420	0.93[AFR][1000 genomes]
rs7641173	0.88[AFR][1000 genomes]
rs7643923	0.91[AFR][1000 genomes]
rs7648096	0.82[AFR][1000 genomes]
rs7650707	0.88[AFR][1000 genomes]
rs7653652	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9310072	0.90[AFR][1000 genomes]
rs9310077	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9813894	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9814057	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9829873	0.82[AFR][1000 genomes]
rs9834468	0.86[AFR][1000 genomes]
rs9835771	0.82[AFR][1000 genomes]
rs9836364	0.92[AFR][1000 genomes]
rs9845776	0.82[AFR][1000 genomes]
rs9847019	0.82[AFR][1000 genomes]
rs9854138	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9865335	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9865578	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9865703	0.83[EUR][1000 genomes]
rs9865710	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9872602	0.82[AFR][1000 genomes]
rs9881255	0.90[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9815738	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs9815738	C3orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88199800-88216800	Weak transcription	Esophagus	oesophagus
2	chr3:88200200-88205600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:88200800-88204800	Weak transcription	Right Ventricle	heart
4	chr3:88200800-88205200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:88200800-88209400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:88200800-88214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:88200800-88218000	Weak transcription	Pancreas	Pancrea
8	chr3:88200800-88221600	Weak transcription	Psoas Muscle	Psoas
9	chr3:88200800-88224400	Weak transcription	Aorta	Aorta
10	chr3:88201000-88205200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:88201200-88204800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:88201200-88205200	Weak transcription	Brain Angular Gyrus	brain
13	chr3:88201200-88205200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:88201200-88205200	Weak transcription	HSMMtube	muscle
15	chr3:88201200-88205200	Weak transcription	K562	blood
16	chr3:88201200-88205400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:88201200-88205800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:88201200-88206400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:88201200-88209600	Weak transcription	Stomach Mucosa	stomach
20	chr3:88201400-88205000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:88201400-88205000	Weak transcription	Hela-S3	cervix
22	chr3:88201400-88205200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:88201400-88212200	Weak transcription	Colonic Mucosa	Colon
24	chr3:88202000-88204800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:88202000-88205600	Weak transcription	Fetal Heart	heart
26	chr3:88202000-88206400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:88202000-88208200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:88202000-88208400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:88202000-88210200	Strong transcription	Placenta	Placenta
30	chr3:88202000-88211400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:88202200-88206000	Strong transcription	Fetal Muscle Leg	muscle
32	chr3:88202200-88208200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:88202200-88208200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:88202200-88208200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:88202200-88208200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:88202200-88209200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:88202200-88211000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:88202200-88211800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:88202200-88212000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:88202400-88205200	Weak transcription	Fetal Brain Male	brain
41	chr3:88202400-88205400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:88202400-88205600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:88202400-88205800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:88202400-88205800	Strong transcription	Left Ventricle	heart
45	chr3:88202400-88206000	Strong transcription	Brain Anterior Caudate	brain
46	chr3:88202400-88206200	Strong transcription	NHEK	skin
47	chr3:88202400-88206600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:88202400-88206800	Strong transcription	Fetal Lung	lung
49	chr3:88202400-88207000	Strong transcription	NH-A	brain
50	chr3:88202400-88207400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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