Variant report

Variant	rs6775666
Chromosome Location	chr3:51703064-51703065
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	CTCF	chr3:51703030-51703880	HCT-116	colon:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
7	POLR2A	chr3:51701652-51704100	K562	blood:	n/a	n/a
8	RAD21	chr3:51702829-51703860	SK-N-SH	brain:	n/a	chr3:51703461-51703475 chr3:51703457-51703476 chr3:51703460-51703473 chr3:51703461-51703471
9	MXI1	chr3:51702898-51703696	IMR90	lung:	n/a	n/a
10	ELF1	chr3:51702971-51703278	K562	blood:	n/a	n/a
11	POLR2A	chr3:51702869-51703119	H1-hESC	embryonic stem cell:	n/a	n/a
12	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: 25 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1055429	0.84[AMR][1000 genomes]
rs11130293	0.80[AMR][1000 genomes]
rs11721253	0.80[AMR][1000 genomes]
rs11917683	0.84[CEU][hapmap]
rs11919197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13090011	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1552074	0.85[AFR][1000 genomes]
rs3821829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4067	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4234644	0.84[CEU][hapmap]
rs4317086	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4355273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4468965	0.83[EUR][1000 genomes]
rs4687569	0.80[AFR][1000 genomes]
rs4687721	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes]
rs4687734	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687770	0.92[CEU][hapmap]
rs4687771	0.92[CEU][hapmap]
rs6445791	0.81[AMR][1000 genomes]
rs6771491	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787312	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6809155	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7372658	0.81[AFR][1000 genomes];0.80[AMR][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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6775666	TEX264	cis	Stomach	GTEx
rs6775666	PARP3	cis	parietal	SCAN
rs6775666	HEMK1	cis	cerebellum	SCAN
rs6775666	TEX264	cis	Artery Tibial	GTEx
rs6775666	TEX264	cis	Esophagus Muscularis	GTEx
rs6775666	HCFC1R1	trans	parietal	SCAN
rs6775666	TEX264	cis	Nerve Tibial	GTEx
rs6775666	RNF123	cis	parietal	SCAN

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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