Variant report

Variant	rs6419866
Chromosome Location	chr3:88215169-88215170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88208458..88210764-chr3:88214434..88217147,2	K562	blood:
2	chr3:88214703..88217502-chr3:88217725..88219491,2	MCF-7	breast:
3	chr3:88205533..88207437-chr3:88214067..88216024,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf38-3	chr3:88210584-88216245	NONHSAT090702

Variant related genes	Relation type
ENSG00000179021	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs13067419	0.92[AFR][1000 genomes]
rs3890707	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4241551	0.90[AFR][1000 genomes]
rs4257571	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4276211	0.90[AFR][1000 genomes]
rs4276212	0.91[AFR][1000 genomes]
rs4337654	0.81[EUR][1000 genomes]
rs4374552	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4378991	0.82[AFR][1000 genomes]
rs4384978	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4402954	0.87[AFR][1000 genomes]
rs4407422	0.83[AFR][1000 genomes]
rs4414876	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4416403	0.82[AFR][1000 genomes]
rs4429658	0.90[AFR][1000 genomes]
rs4432672	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4434168	0.90[AFR][1000 genomes]
rs4438681	0.82[AFR][1000 genomes]
rs4485742	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4488864	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4501136	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4507280	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4518156	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4555548	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4568164	0.88[AFR][1000 genomes]
rs4580585	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4596173	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4616670	0.90[AFR][1000 genomes]
rs4858935	0.85[EUR][1000 genomes]
rs4858936	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4858995	0.90[AFR][1000 genomes]
rs4858997	0.85[AFR][1000 genomes]
rs4859001	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6419867	0.86[EUR][1000 genomes]
rs6551268	0.82[AFR][1000 genomes]
rs6551271	0.90[AFR][1000 genomes]
rs6551272	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6551274	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6551275	0.84[EUR][1000 genomes]
rs6551277	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6551278	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6551279	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6551280	0.83[EUR][1000 genomes]
rs6551282	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6551283	0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6551284	0.97[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6551285	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6551286	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6551288	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6551289	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6551291	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6781333	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6782507	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6785359	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6786788	0.90[AFR][1000 genomes]
rs6787824	0.92[AFR][1000 genomes]
rs6790629	0.81[AFR][1000 genomes]
rs6791133	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6792208	0.90[AFR][1000 genomes]
rs6793783	0.90[AFR][1000 genomes]
rs6795209	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6796355	0.93[AFR][1000 genomes]
rs6799233	0.82[AFR][1000 genomes]
rs6804818	0.90[AFR][1000 genomes]
rs6805804	0.83[AFR][1000 genomes]
rs6805908	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs71616896	0.82[AMR][1000 genomes]
rs7427704	0.93[AFR][1000 genomes]
rs7429120	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7430158	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7432838	0.83[EUR][1000 genomes]
rs7433285	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7617691	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7618080	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7618472	0.82[AFR][1000 genomes]
rs7620130	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7626777	0.90[AFR][1000 genomes]
rs7628689	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7630028	0.92[AFR][1000 genomes]
rs7630240	0.93[AFR][1000 genomes]
rs7632123	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7635996	0.87[AFR][1000 genomes]
rs7637431	0.89[EUR][1000 genomes]
rs7639420	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7641173	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7643923	0.92[AFR][1000 genomes]
rs7648096	0.82[AFR][1000 genomes]
rs7650707	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7653652	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9310072	0.90[AFR][1000 genomes]
rs9310077	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9813894	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9814057	0.97[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9815738	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9829873	0.82[AFR][1000 genomes]
rs9834468	0.87[AFR][1000 genomes]
rs9835771	0.82[AFR][1000 genomes]
rs9836364	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9845776	0.82[AFR][1000 genomes]
rs9847019	0.82[AFR][1000 genomes]
rs9847322	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9854138	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9865335	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9865578	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9865703	0.84[EUR][1000 genomes]
rs9865710	0.94[AFR][1000 genomes];0.84[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
rs6419866	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs6419866	C3orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88199800-88216800	Weak transcription	Esophagus	oesophagus
2	chr3:88200800-88218000	Weak transcription	Pancreas	Pancrea
3	chr3:88200800-88221600	Weak transcription	Psoas Muscle	Psoas
4	chr3:88200800-88224400	Weak transcription	Aorta	Aorta
5	chr3:88204400-88217400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:88205600-88217600	Weak transcription	Fetal Intestine Small	intestine
7	chr3:88205600-88222000	Weak transcription	Fetal Stomach	stomach
8	chr3:88205600-88222800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:88205800-88217800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:88205800-88220200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:88205800-88227000	Weak transcription	Lung	lung
12	chr3:88205800-88232400	Weak transcription	Left Ventricle	heart
13	chr3:88206000-88217800	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:88206000-88226800	Weak transcription	Ovary	ovary
15	chr3:88206000-88229800	Weak transcription	Thymus	Thymus
16	chr3:88206200-88221200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:88206200-88221800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:88206600-88217400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:88206800-88223400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:88207400-88222200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:88208000-88215400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:88208000-88218800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:88208200-88215800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:88208200-88216000	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:88208200-88216200	Weak transcription	Fetal Intestine Large	intestine
26	chr3:88208200-88217000	Weak transcription	A549	lung
27	chr3:88208200-88217000	Weak transcription	GM12878-XiMat	blood
28	chr3:88208200-88217200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:88208200-88217200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:88208200-88220400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:88208200-88224600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:88208200-88226600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:88208400-88220400	Weak transcription	Brain Germinal Matrix	brain
34	chr3:88208600-88216200	Weak transcription	K562	blood
35	chr3:88208600-88217400	Weak transcription	Fetal Thymus	thymus
36	chr3:88209200-88226400	Weak transcription	Primary B cells from cord blood	blood
37	chr3:88209200-88227800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:88210000-88221800	Weak transcription	Liver	Liver
39	chr3:88210800-88218000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:88211000-88216600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:88211000-88223800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:88211200-88218000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:88211800-88217000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:88212000-88216200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:88212000-88221400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:88212200-88217000	Weak transcription	Osteobl	bone
47	chr3:88212200-88217200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:88212200-88222800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:88212400-88216600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:88212400-88217200	Weak transcription	Primary B cells from peripheral blood	blood

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