Variant report

Variant	rs10947058
Chromosome Location	chr6:30176122-30176123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:183)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr6:30174205-30176177	HepG2	liver:	n/a	n/a
2	GATA3	chr6:30175667-30176177	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:30174571-30176242	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:30175849-30176207	GM12878	blood:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30176093-30176143	ECC-1	luminal epithelium:	n/a
2	chr6:30176107-30176157	BE2_C	brain:	n/a
3	chr6:30176076-30176126	HCF	heart:	n/a
4	chr6:30176093-30176143	HRE	kidney:	n/a
5	chr6:30176093-30176143	SAEC	small airway:	n/a
6	chr6:30176107-30176157	T-47D	breast:	n/a
7	chr6:30176107-30176157	HNPCEpiC	eye:	n/a
8	chr6:30176093-30176143	HCF	heart:	n/a
9	chr6:30176093-30176143	HCT-116	colon:	n/a
10	chr6:30176107-30176157	Jurkat	blood:	n/a
11	chr6:30176076-30176126	HNPCEpiC	eye:	n/a
12	chr6:30176107-30176157	CMK	blood:	n/a
13	chr6:30176093-30176143	SKMC	muscle:	n/a
14	chr6:30176107-30176157	NHBE	bronchial:	n/a
15	chr6:30176076-30176126	GM12878	blood:	n/a
16	chr6:30176093-30176143	HEK293	kidney:	embryo
17	chr6:30176076-30176126	HCT-116	colon:	n/a
18	chr6:30176107-30176157	HCF	heart:	n/a
19	chr6:30176093-30176143	NB4	blood:	n/a
20	chr6:30176093-30176143	GM06990	blood:	n/a
21	chr6:30176093-30176143	HRPEpiC	eye:	n/a
22	chr6:30176093-30176143	HCM	heart:	n/a
23	chr6:30176107-30176157	RPTEC	kidney:	n/a
24	chr6:30176076-30176126	BJ	skin:	n/a
25	chr6:30176093-30176143	HMEC	breast:	n/a
26	chr6:30176107-30176157	HIPEpiC	eye:	n/a
27	chr6:30176107-30176157	HAEpiC	amniotic membrane:	n/a
28	chr6:30176093-30176143	HUVEC	blood vessel:	n/a
29	chr6:30176093-30176143	U87	brain:	n/a
30	chr6:30176107-30176157	Hela-S3	cervix:	n/a
31	chr6:30176076-30176126	NB4	blood:	n/a
32	chr6:30176093-30176143	PFSK-1	brain:	n/a
33	chr6:30176093-30176143	AG10803	skin:	n/a
34	chr6:30176076-30176126	GM19239	blood:	n/a
35	chr6:30176076-30176126	PFSK-1	brain:	n/a
36	chr6:30176076-30176126	Caco-2	colon:	n/a
37	chr6:30176093-30176143	Caco-2	colon:	n/a
38	chr6:30176076-30176126	HRCEpiC	kidney:	n/a
39	chr6:30176076-30176126	ProgFib	skin:	n/a
40	chr6:30176107-30176157	NT2-D1	testis:	n/a
41	chr6:30176093-30176143	H1-hESC	embryonic stem cell:	embryo
42	chr6:30176076-30176126	ovcar-3	ovarian:	n/a
43	chr6:30176076-30176126	AoSMC	blood vessel:	n/a
44	chr6:30176093-30176143	PANC-1	pancreas:	n/a
45	chr6:30176107-30176157	ECC-1	luminal epithelium:	n/a
46	chr6:30176093-30176143	RPTEC	kidney:	n/a
47	chr6:30176107-30176157	PFSK-1	brain:	n/a
48	chr6:30176093-30176143	GM12892	blood:	n/a
49	chr6:30176107-30176157	NHDF-neo	bronchial:	n/a
50	chr6:30176107-30176157	SAEC	small airway:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30112108..30113874-chr6:30174193..30176985,2	K562	blood:
2	chr6:30153704..30155997-chr6:30174654..30176677,2	MCF-7	breast:
3	chr6:30168209..30170458-chr6:30175226..30176879,2	MCF-7	breast:
4	chr6:30176086..30179759-chr6:30179877..30183202,4	K562	blood:
5	chr6:30166782..30168897-chr6:30174962..30177557,2	K562	blood:
6	chr6:30027540..30029604-chr6:30175279..30176794,2	MCF-7	breast:
7	chr6:30175583..30179292-chr6:30184478..30187344,3	K562	blood:
8	chr6:30170611..30172995-chr6:30173743..30176690,2	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM26	TF binding region
TRIM26	CpG island
ENSG00000204623	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000066379	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11753736	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758350	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192345	0.98[EUR][1000 genomes]
rs12212092	1.00[ASN][1000 genomes]
rs1264622	1.00[ASN][1000 genomes]
rs13212414	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213365	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215307	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16897204	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516722	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844753	1.00[ASN][1000 genomes]
rs34366388	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920344	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942037	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928824	1.00[ASN][1000 genomes]
rs9295837	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501426	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501427	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501428	0.88[AFR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10947058	HLA-H	cis	multi-tissue	Pritchard
rs10947058	ZFP57	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
3	chr6:30167000-30178000	Weak transcription	Fetal Brain Female	brain
4	chr6:30168800-30179800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:30169000-30179800	Weak transcription	Aorta	Aorta
6	chr6:30170200-30179200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:30170600-30179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:30171600-30176200	Strong transcription	Primary T cells from cord blood	blood
9	chr6:30172400-30179200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:30172600-30176800	Weak transcription	Dnd41	blood
11	chr6:30172600-30178400	Enhancers	Esophagus	oesophagus
12	chr6:30172600-30179800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:30173000-30176200	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr6:30173000-30176200	Enhancers	Fetal Heart	heart
15	chr6:30173000-30177200	Strong transcription	Thymus	Thymus
16	chr6:30173000-30179200	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr6:30173200-30178400	Enhancers	Pancreas	Pancrea
18	chr6:30173400-30176200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:30173400-30176200	Enhancers	Left Ventricle	heart
20	chr6:30173400-30179600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr6:30173400-30179800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:30173400-30179800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:30173600-30176200	Enhancers	Psoas Muscle	Psoas
24	chr6:30173600-30176600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:30173800-30176200	Enhancers	Osteobl	bone
26	chr6:30173800-30176600	Enhancers	NHDF-Ad	bronchial
27	chr6:30173800-30179800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr6:30173800-30180000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:30174000-30176200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:30174000-30176200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:30174000-30176200	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr6:30174000-30176200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:30174000-30176200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:30174000-30176200	Enhancers	Adipose Nuclei	Adipose
35	chr6:30174000-30176200	Enhancers	Brain Angular Gyrus	brain
36	chr6:30174000-30176200	Enhancers	Brain Cingulate Gyrus	brain
37	chr6:30174000-30176200	Enhancers	Right Ventricle	heart
38	chr6:30174000-30176600	Flanking Active TSS	HepG2	liver
39	chr6:30174000-30176600	Enhancers	NHLF	lung
40	chr6:30174000-30176800	Enhancers	HMEC	breast
41	chr6:30174000-30177200	Enhancers	Fetal Intestine Large	intestine
42	chr6:30174200-30176200	Flanking Active TSS	Liver	Liver
43	chr6:30174400-30176200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr6:30174400-30176200	Enhancers	Fetal Muscle Leg	muscle
45	chr6:30174400-30176400	Enhancers	Fetal Kidney	kidney
46	chr6:30174400-30177400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
47	chr6:30174600-30176200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:30174600-30176200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:30174600-30176200	Enhancers	H9 Cell Line	embryonic stem cell
50	chr6:30174600-30176200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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