Variant report

Variant	rs9824779
Chromosome Location	chr3:51703025-51703026
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	CTCF	chr3:51703000-51703150	GM12868	blood:	n/a	n/a
2	CTCF	chr3:51702940-51703090	GM12874	blood:	n/a	n/a
3	CTCF	chr3:51703000-51703150	GM12873	blood:	n/a	n/a
4	MXI1	chr3:51702935-51703859	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr3:51702691-51704450	SK-N-SH	brain:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
6	POLR2A	chr3:51701652-51704100	K562	blood:	n/a	n/a
7	RAD21	chr3:51702829-51703860	SK-N-SH	brain:	n/a	chr3:51703461-51703475 chr3:51703457-51703476 chr3:51703460-51703473 chr3:51703461-51703471
8	MXI1	chr3:51702898-51703696	IMR90	lung:	n/a	n/a
9	ELF1	chr3:51702971-51703278	K562	blood:	n/a	n/a
10	POLR2A	chr3:51702869-51703119	H1-hESC	embryonic stem cell:	n/a	n/a
11	SMC3	chr3:51702722-51703739	SK-N-SH	brain:	n/a	chr3:51703461-51703471 chr3:51703468-51703475 chr3:51703049-51703056 chr3:51703464-51703472 chr3:51703461-51703475

No.	Distal block	Cell Line	Cell type
1	chr3:51689639..51691996-chr3:51702378..51704180,2	K562	blood:
2	chr3:51692768..51695628-chr3:51701276..51703775,2	K562	blood:
3	chr3:51694128..51695719-chr3:51702275..51704283,2	K562	blood:
4	chr3:51532096..51536424-chr3:51702408..51707498,7	K562	blood:
5	chr3:51702918..51706936-chr3:51707889..51711767,6	MCF-7	breast:

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

Variant related genes	Relation type
TEX264	TF binding region
ENSG00000145041	Chromatin interaction
ENSG00000164081	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs12330534	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13314120	0.91[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];1.00[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]
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];0.91[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];1.00[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	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	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	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	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	1.00[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	0.82[AFR][1000 genomes];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	0.81[AFR][1000 genomes];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]
rs9809757	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]
rs9812008	0.91[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	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.86[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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838294	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.88[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	0.91[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];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	0.91[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	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	0.91[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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	1.00[YRI][hapmap];1.00[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];0.81[AFR][1000 genomes];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];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	1.00[AMR][1000 genomes]
rs9882601	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv965167	chr3:51702892-51707059	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr3:51681600-51703200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:51682200-51704400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:51690800-51704400	Weak transcription	HUVEC	blood vessel
4	chr3:51694200-51704800	Weak transcription	Psoas Muscle	Psoas
5	chr3:51694400-51704400	Weak transcription	Fetal Brain Male	brain
6	chr3:51694400-51704600	Weak transcription	NHDF-Ad	bronchial
7	chr3:51696200-51704400	Weak transcription	Fetal Kidney	kidney
8	chr3:51696600-51704200	Weak transcription	Small Intestine	intestine
9	chr3:51697200-51703200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:51697200-51704600	Weak transcription	Brain Substantia Nigra	brain
11	chr3:51697400-51703200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:51697400-51703400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:51697400-51703600	Weak transcription	GM12878-XiMat	blood
14	chr3:51697400-51704400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:51697400-51704400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:51697400-51704600	Weak transcription	Left Ventricle	heart
17	chr3:51697400-51704800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:51697400-51704800	Weak transcription	Aorta	Aorta
19	chr3:51697600-51703200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:51697600-51704400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:51697800-51703200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:51697800-51703200	Weak transcription	NHLF	lung
23	chr3:51697800-51704400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:51697800-51704600	Weak transcription	HSMM	muscle
25	chr3:51698000-51703200	Weak transcription	Thymus	Thymus
26	chr3:51698000-51703400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:51698000-51703400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:51698000-51703600	Weak transcription	Gastric	stomach
29	chr3:51698000-51704800	Weak transcription	Ovary	ovary
30	chr3:51698200-51703200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:51698200-51704600	Weak transcription	NH-A	brain
32	chr3:51698400-51703200	Weak transcription	Fetal Intestine Small	intestine
33	chr3:51698400-51703400	Weak transcription	Adipose Nuclei	Adipose
34	chr3:51698400-51703400	Weak transcription	Spleen	Spleen
35	chr3:51698400-51704400	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:51698400-51704600	Weak transcription	HSMMtube	muscle
37	chr3:51699400-51703200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:51699400-51704400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:51699800-51704400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:51699800-51704400	Weak transcription	Brain Germinal Matrix	brain
41	chr3:51700000-51703200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:51700000-51703200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:51700000-51703800	Weak transcription	Lung	lung
44	chr3:51700000-51704400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:51700000-51704400	Weak transcription	Fetal Intestine Large	intestine
46	chr3:51700000-51704600	Weak transcription	Fetal Brain Female	brain
47	chr3:51700200-51703800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:51700600-51703200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:51700600-51704600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:51701200-51704400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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