Variant report

Variant	rs9809757
Chromosome Location	chr3:51700559-51700560
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51699216..51703004-chr3:51704481..51706948,3	MCF-7	breast:
2	chr3:51699532..51702508-chr3:51709251..51711511,2	MCF-7	breast:
3	chr3:51432016..51433899-chr3:51699483..51701969,2	MCF-7	breast:
4	chr3:51696120..51698104-chr3:51700426..51702276,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IQCF6-2	chr3:51700250-51703672	NONHSAT089874

Variant related genes	Relation type
ENSG00000164081	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12330534	1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13314120	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13321674	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13325153	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[YRI][hapmap]
rs13327225	1.00[MEX][hapmap]
rs13433729	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051799	1.00[AMR][1000 genomes]
rs17051802	1.00[ASW][hapmap]
rs17051832	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421789	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28452990	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	1.00[AMR][1000 genomes]
rs28653367	1.00[AMR][1000 genomes]
rs2883900	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549265	1.00[AMR][1000 genomes]
rs56942057	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6792143	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs6806124	1.00[MEX][hapmap]
rs72951441	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9808940	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815475	1.00[MEX][hapmap]
rs9815684	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	1.00[AMR][1000 genomes]
rs9827917	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838294	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839516	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840331	1.00[AMR][1000 genomes]
rs9842066	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855809	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857893	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858497	1.00[AMR][1000 genomes]
rs9864213	1.00[AMR][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878564	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9880050	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880909	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882601	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51680800-51702800	Weak transcription	K562	blood
2	chr3:51681600-51703200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:51682200-51704400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:51682600-51702800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:51688000-51701000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:51688000-51701800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:51688000-51702200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:51688000-51702400	Strong transcription	Fetal Stomach	stomach
9	chr3:51688600-51701200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:51688800-51700600	Strong transcription	Stomach Smooth Muscle	stomach
11	chr3:51689000-51700600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:51689800-51702600	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:51689800-51703000	Weak transcription	Fetal Heart	heart
14	chr3:51690400-51703000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:51690800-51704400	Weak transcription	HUVEC	blood vessel
16	chr3:51694200-51704800	Weak transcription	Psoas Muscle	Psoas
17	chr3:51694400-51704400	Weak transcription	Fetal Brain Male	brain
18	chr3:51694400-51704600	Weak transcription	NHDF-Ad	bronchial
19	chr3:51694600-51700600	Strong transcription	Liver	Liver
20	chr3:51695600-51702800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:51695800-51703000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:51696200-51704400	Weak transcription	Fetal Kidney	kidney
23	chr3:51696600-51704200	Weak transcription	Small Intestine	intestine
24	chr3:51697000-51702800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:51697200-51703200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:51697200-51704600	Weak transcription	Brain Substantia Nigra	brain
27	chr3:51697400-51702400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:51697400-51702800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:51697400-51702800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:51697400-51703000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:51697400-51703000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:51697400-51703000	Weak transcription	A549	lung
33	chr3:51697400-51703200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:51697400-51703400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:51697400-51703600	Weak transcription	GM12878-XiMat	blood
36	chr3:51697400-51704400	Weak transcription	Brain Angular Gyrus	brain
37	chr3:51697400-51704400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:51697400-51704600	Weak transcription	Left Ventricle	heart
39	chr3:51697400-51704800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:51697400-51704800	Weak transcription	Aorta	Aorta
41	chr3:51697600-51703000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:51697600-51703000	Weak transcription	Pancreas	Pancrea
43	chr3:51697600-51703200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:51697600-51704400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:51697800-51700800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:51697800-51702800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:51697800-51702800	Weak transcription	HMEC	breast
48	chr3:51697800-51703000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:51697800-51703000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:51697800-51703000	Weak transcription	Colonic Mucosa	Colon

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