Variant report

Variant	rs6929908
Chromosome Location	chr6:26555289-26555290
allele	A/C
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:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26537344..26540066-chr6:26554422..26557839,4	MCF-7	breast:
2	chr6:26329309..26333130-chr6:26553526..26558565,5	K562	blood:
3	chr6:26550749..26553522-chr6:26553841..26558660,4	K562	blood:
4	chr6:26554929..26556966-chr6:27111412..27114183,2	K562	blood:
5	chr6:26554282..26558961-chr6:26593816..26597710,6	K562	blood:
6	chr6:26205624..26207427-chr6:26554125..26557107,2	MCF-7	breast:
7	chr6:26305449..26307916-chr6:26554674..26557106,2	K562	blood:
8	chr6:26179565..26181746-chr6:26554462..26557282,3	K562	blood:
9	chr6:26552134..26560768-chr6:26592842..26598560,12	K562	blood:
10	chr6:26553266..26555842-chr6:26556342..26558941,2	K562	blood:
11	chr6:26315914..26318204-chr6:26552623..26555591,2	MCF-7	breast:
12	chr6:26310371..26313077-chr6:26554610..26556744,3	K562	blood:
13	chr6:26053729..26056737-chr6:26552684..26556029,5	K562	blood:
14	chr6:26204395..26207558-chr6:26552020..26555399,3	K562	blood:
15	chr6:26215416..26220761-chr6:26552496..26557332,5	K562	blood:
16	chr6:26547747..26549536-chr6:26553157..26556049,2	MCF-7	breast:
17	chr6:26339310..26342101-chr6:26554337..26555953,2	K562	blood:
18	chr6:26327903..26334280-chr6:26553526..26557732,8	K562	blood:
19	chr6:26551841..26553522-chr6:26554319..26556111,2	K562	blood:
20	chr6:26553141..26555933-chr6:26567279..26569954,2	MCF-7	breast:
21	chr6:26554084..26556655-chr6:27114642..27116413,3	K562	blood:
22	chr6:26553067..26555793-chr6:27098246..27101919,3	K562	blood:
23	chr6:26121340..26124270-chr6:26554481..26556338,2	K562	blood:
24	chr6:26187838..26190767-chr6:26553872..26556944,3	K562	blood:
25	chr6:26031374..26034016-chr6:26553380..26556747,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124693	Chromatin interaction
ENSG00000188987	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1535275	0.92[EUR][1000 genomes]
rs1535278	0.90[MKK][hapmap]
rs15580	0.87[LWK][hapmap];1.00[MKK][hapmap]
rs2451715	0.84[JPT][hapmap]
rs2451716	0.84[JPT][hapmap]
rs2451746	0.84[JPT][hapmap]
rs2451752	0.84[JPT][hapmap]
rs2451753	0.84[JPT][hapmap]
rs2494691	0.84[JPT][hapmap]
rs2494705	0.84[JPT][hapmap]
rs2494711	0.84[JPT][hapmap]
rs3736780	0.87[LWK][hapmap];1.00[MKK][hapmap]
rs3800302	0.84[JPT][hapmap]
rs4591839	0.84[JPT][hapmap]
rs4711112	1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4713007	0.87[LWK][hapmap];1.00[MKK][hapmap]
rs6456729	0.82[EUR][1000 genomes]
rs6906521	1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6911330	0.87[LWK][hapmap];1.00[MKK][hapmap]
rs6911540	0.84[JPT][hapmap]
rs6913550	0.94[EUR][1000 genomes]
rs6915555	0.84[JPT][hapmap]
rs6916321	1.00[CEU][hapmap]
rs6919391	0.84[JPT][hapmap]
rs6922256	1.00[LWK][hapmap]
rs6927012	0.86[MKK][hapmap]
rs6931849	0.84[JPT][hapmap]
rs7745632	0.87[LWK][hapmap];1.00[MKK][hapmap]
rs7750131	0.84[EUR][1000 genomes]
rs7765920	1.00[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs9295696	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295697	0.89[AFR][1000 genomes]
rs9357008	0.89[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9379892	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379902	0.84[JPT][hapmap]

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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6929908	RP11-457M11.5	cis	Esophagus Mucosa	GTEx
rs6929908	BTN3A3	cis	cerebellum	SCAN
rs6929908	RP11-457M11.2	cis	Artery Aorta	GTEx
rs6929908	BTN2A1	cis	parietal	SCAN
rs6929908	ABT1	cis	cerebellum	SCAN
rs6929908	DCDC2	cis	cerebellum	SCAN
rs6929908	BTN3A2	cis	cerebellum	SCAN
rs6929908	HIST1H3H	cis	parietal	SCAN
rs6929908	BTN3A2	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26551000-26556400	Weak transcription	Spleen	Spleen
2	chr6:26551200-26556200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:26552600-26556200	Active TSS	GM12878-XiMat	blood
4	chr6:26552600-26556400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr6:26552600-26556800	Active TSS	NHDF-Ad	bronchial
6	chr6:26552800-26556400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:26552800-26557200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:26553000-26556200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:26553000-26557000	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr6:26553000-26557000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:26553000-26557000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:26553000-26557200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:26553000-26557200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:26553000-26557200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:26553000-26557200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:26553000-26557200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr6:26553000-26557200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr6:26553000-26557200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:26553000-26557200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:26553200-26555400	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr6:26553200-26555400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr6:26553200-26555400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr6:26553200-26555400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr6:26553200-26555400	Active TSS	Ovary	ovary
25	chr6:26553200-26555400	Active TSS	Right Ventricle	heart
26	chr6:26553200-26555400	Flanking Active TSS	HUVEC	blood vessel
27	chr6:26553200-26555400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr6:26553200-26555600	Active TSS	Duodenum Mucosa	Duodenum
29	chr6:26553200-26556000	Active TSS	Fetal Intestine Small	intestine
30	chr6:26553200-26556000	Active TSS	Right Atrium	heart
31	chr6:26553200-26556400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:26553200-26556400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:26553200-26556400	Active TSS	NHLF	lung
34	chr6:26553200-26556600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:26553200-26556600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:26553200-26556600	Active TSS	Fetal Muscle Trunk	muscle
37	chr6:26553200-26556800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr6:26553200-26556800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:26553200-26556800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:26553200-26556800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:26553200-26556800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:26553200-26557000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:26553200-26557000	Active TSS	A549	lung
44	chr6:26553200-26557200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:26553400-26555400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:26553400-26555400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:26553400-26555400	Bivalent/Poised TSS	HepG2	liver
48	chr6:26553400-26555800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:26553400-26556400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:26553400-26556600	Active TSS	Brain Anterior Caudate	brain

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