Variant report

Variant	rs3800302
Chromosome Location	chr6:26597333-26597334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26155821..26161666-chr6:26595746..26599191,6	K562	blood:
2	chr6:26123945..26125914-chr6:26596676..26599538,2	MCF-7	breast:
3	chr6:26594524..26600977-chr6:27096034..27104390,19	K562	blood:
4	chr4:99944161..99945674-chr6:26596054..26598932,3	K562	blood:
5	chr6:26586123..26588537-chr6:26597287..26599098,2	K562	blood:
6	chr6:26285546..26288000-chr6:26593708..26598025,4	K562	blood:
7	chr6:26596362..26598030-chr6:26986586..26989465,2	MCF-7	breast:
8	chr19:40336233..40337167-chr6:26596570..26597367,2	HCT-116	colon:
9	chr6:26593362..26600987-chr6:27097692..27106488,18	K562	blood:
10	chr6:26595597..26597403-chr6:26659467..26661984,2	MCF-7	breast:
11	chr6:26500256..26501997-chr6:26596237..26599100,2	K562	blood:
12	chr4:99942655..99945658-chr6:26596311..26598592,3	MCF-7	breast:
13	chr4:99944149..99944674-chr6:26596172..26597619,4	HCT-116	colon:
14	chr6:26595623..26599966-chr6:27100615..27102925,4	MCF-7	breast:
15	chr4:99944168..99944674-chr6:26597086..26597613,2	MCF-7	breast:
16	chr6:26157345..26159809-chr6:26595346..26597752,3	K562	blood:
17	chr6:26536174..26539515-chr6:26593643..26598624,4	K562	blood:
18	chr4:99942650..99945674-chr6:26595832..26598932,6	K562	blood:
19	chr6:26122958..26124980-chr6:26596151..26598779,2	K562	blood:
20	chr6:26054694..26056843-chr6:26595582..26598310,3	MCF-7	breast:
21	chr6:26593150..26599498-chr6:27112360..27118946,12	K562	blood:
22	chr6:26595534..26598582-chr6:27105401..27109406,3	K562	blood:
23	chr6:26535400..26541597-chr6:26593643..26598951,8	K562	blood:
24	chr6:26595477..26598975-chr6:26986599..26989051,3	K562	blood:
25	chr6:26520764..26524239-chr6:26594606..26597481,4	K562	blood:
26	chr4:99944145..99944678-chr6:26597051..26597713,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198339	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000181315	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000250496	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000224843	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000238621	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000124557	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2451714	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2451715	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2451716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2451739	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2451742	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2451746	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2451749	0.83[EUR][1000 genomes]
rs2451752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2451753	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2451754	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2494691	0.96[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2494705	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2494706	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2494710	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2494711	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2498342	0.95[CHB][hapmap];0.92[JPT][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2498343	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3807029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4591839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456738	0.80[ASN][1000 genomes]
rs6456739	0.93[ASN][1000 genomes]
rs6902411	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6911540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915555	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929908	0.84[JPT][hapmap]
rs6931849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379892	0.84[JPT][hapmap]
rs9379902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379903	0.99[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs3800302	ZNF322	cis	Artery Tibial	GTEx
rs3800302	BTN2A2	cis	cerebellum	SCAN
rs3800302	RP11-457M11.2	cis	Thyroid	GTEx
rs3800302	ZNF204P	cis	cerebellum	SCAN
rs3800302	BTN3A2	cis	parietal	SCAN
rs3800302	RP11-457M11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs3800302	BTN3A2	cis	cerebellum	SCAN
rs3800302	RP11-457M11.2	cis	Artery Tibial	GTEx
rs3800302	BTN3A3	cis	cerebellum	SCAN
rs3800302	HIST1H3E	cis	cerebellum	SCAN
rs3800302	HIST1H4L	cis	parietal	SCAN
rs3800302	ZNF322	cis	Thyroid	GTEx
rs3800302	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs3800302	ZNF322	cis	Nerve Tibial	GTEx
rs3800302	RP11-457M11.2	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26593000-26598000	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:26593000-26598400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:26593600-26598400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:26593800-26598000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr6:26593800-26598000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:26593800-26598000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:26593800-26598000	Active TSS	A549	lung
8	chr6:26593800-26598200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:26593800-26598200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:26593800-26598600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr6:26594000-26598000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:26594000-26598000	Active TSS	K562	blood
13	chr6:26594000-26598200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:26594200-26598400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:26594200-26598400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:26594400-26597800	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr6:26594400-26598000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:26594400-26598000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:26594400-26598200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:26594600-26598000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:26594600-26598400	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:26594800-26598400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:26595200-26597800	Active TSS	Brain Angular Gyrus	brain
24	chr6:26595200-26597800	Active TSS	Brain Cingulate Gyrus	brain
25	chr6:26595200-26597800	Active TSS	Brain Substantia Nigra	brain
26	chr6:26595200-26598000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:26595200-26598000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:26595200-26598000	Active TSS	Ovary	ovary
29	chr6:26595200-26598000	Active TSS	GM12878-XiMat	blood
30	chr6:26595400-26597800	Active TSS	Brain Anterior Caudate	brain
31	chr6:26595400-26598000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:26595600-26597600	Active TSS	Primary T cells from cord blood	blood
33	chr6:26595600-26597600	Bivalent/Poised TSS	Fetal Brain Female	brain
34	chr6:26595600-26597800	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr6:26595600-26597800	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr6:26595600-26597800	Active TSS	Fetal Lung	lung
37	chr6:26595600-26598000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:26595600-26598000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:26595600-26598000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:26595600-26598000	Active TSS	Aorta	Aorta
41	chr6:26595600-26598000	Active TSS	Left Ventricle	heart
42	chr6:26595600-26598000	Active TSS	Right Ventricle	heart
43	chr6:26595600-26598200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:26595600-26598200	Active TSS	HSMMtube	muscle
45	chr6:26595600-26598400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:26595800-26597800	Active TSS	Brain Hippocampus Middle	brain
47	chr6:26595800-26597800	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr6:26595800-26597800	Active TSS	Colon Smooth Muscle	Colon
49	chr6:26595800-26597800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:26595800-26598000	Active TSS	NHDF-Ad	bronchial

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