Variant report

Variant	rs11968825
Chromosome Location	chr6:27357721-27357722
allele	A/T
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:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27113785..27116304-chr6:27356399..27358052,2	K562	blood:
2	chr6:27356277..27359093-chr6:27439899..27443040,4	MCF-7	breast:
3	chr6:27114804..27117756-chr6:27356552..27360776,4	K562	blood:
4	chr6:27357105..27360959-chr6:27363374..27365305,4	K562	blood:
5	chr6:27356362..27358956-chr6:27773296..27775539,3	K562	blood:
6	chr6:27341304..27343058-chr6:27356076..27357820,2	MCF-7	breast:
7	chr6:27342371..27343890-chr6:27355850..27358027,2	K562	blood:
8	chr6:27356907..27359078-chr6:27397692..27399728,2	K562	blood:
9	chr6:27291445..27294642-chr6:27355178..27358043,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRSS16-2	chr6:27357718-27358702	NONHSAT108380

No data

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000220758	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1014227	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1022515	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10484398	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10755644	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10807020	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10807021	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10807024	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs10807025	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10946913	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10946914	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10946920	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10946921	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10946931	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10946932	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10946933	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12199110	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12213598	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12662076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13201443	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13201965	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13201985	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs13220155	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1534937	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1883216	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1883404	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1883405	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1985818	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2015648	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2049945	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2064219	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2076305	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2092121	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2092122	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2142705	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2143062	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2179154	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2206250	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2206251	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2206252	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2223463	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2223464	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2235252	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2235254	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2272814	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2294308	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2294309	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2393929	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2393931	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2893917	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3734574	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3734575	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4305708	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4358616	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4455661	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4478400	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4504471	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4562132	0.93[CEU][hapmap]
rs4711147	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711148	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711153	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4713086	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4713092	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4713105	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4713106	0.86[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs6456774	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6456777	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6456778	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6456781	0.86[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs6456785	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6456788	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6456790	0.81[CEU][hapmap]
rs6650992	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6899950	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6904883	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6915934	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6920010	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6920362	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6920408	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6920733	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6921071	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6923108	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6923539	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6929812	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6934748	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6934985	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6936356	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6936539	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6938943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs726830	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7509	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs764460	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs766092	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7741031	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7744110	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7745380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7748366	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7750795	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7754411	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7754678	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7754724	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7754977	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7759001	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7761989	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7772160	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7774613	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9348765	0.81[JPT][hapmap]
rs9357037	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9368503	0.80[JPT][hapmap]
rs9461380	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9468101	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9468111	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9468115	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9468117	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9468141	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs980960	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs980961	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs980962	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs980963	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1031803	chr6:27355881-27423655	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538166	chr6:27355881-27423655	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11968825	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs11968825	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs11968825	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27355600-27358400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:27355800-27357800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27355800-27357800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:27355800-27357800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:27355800-27357800	Active TSS	GM12878-XiMat	blood
6	chr6:27355800-27358000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:27355800-27358000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:27356000-27357800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:27356000-27357800	Active TSS	Primary B cells from cord blood	blood
10	chr6:27356200-27357800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:27356200-27357800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:27356200-27357800	Active TSS	Primary T cells from cord blood	blood
13	chr6:27356200-27358000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr6:27356800-27357800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:27356800-27358000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:27357000-27358000	Flanking Active TSS	Dnd41	blood
17	chr6:27357200-27357800	Enhancers	Spleen	Spleen
18	chr6:27357200-27358200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:27357200-27362200	Weak transcription	Aorta	Aorta
20	chr6:27357200-27366600	Weak transcription	Left Ventricle	heart
21	chr6:27357400-27357800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:27357400-27357800	Active TSS	Adipose Nuclei	Adipose
23	chr6:27357400-27357800	Enhancers	Brain Cingulate Gyrus	brain
24	chr6:27357400-27357800	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:27357400-27357800	Active TSS	Duodenum Mucosa	Duodenum
26	chr6:27357400-27357800	Enhancers	HMEC	breast
27	chr6:27357400-27357800	Active TSS	Monocytes-CD14+_RO01746	blood
28	chr6:27357400-27358200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:27357400-27361600	Weak transcription	Colonic Mucosa	Colon
30	chr6:27357400-27363000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:27357400-27363000	Weak transcription	Right Atrium	heart
32	chr6:27357400-27364200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:27357400-27364800	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:27357400-27364800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:27357400-27365000	Weak transcription	Fetal Lung	lung
36	chr6:27357400-27366000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:27357400-27367000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:27357400-27367200	Weak transcription	Brain Substantia Nigra	brain
39	chr6:27357400-27367800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:27357400-27368000	Weak transcription	Fetal Kidney	kidney
41	chr6:27357600-27357800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr6:27357600-27357800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:27357600-27357800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr6:27357600-27357800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:27357600-27357800	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr6:27357600-27357800	Flanking Active TSS	K562	blood
47	chr6:27357600-27357800	Flanking Active TSS	NHEK	skin
48	chr6:27357600-27358000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr6:27357600-27358000	Enhancers	Brain Hippocampus Middle	brain
50	chr6:27357600-27358000	Enhancers	Hela-S3	cervix

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