Variant report

Variant	rs10484549
Chromosome Location	chr6:30026290-30026291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30026282-30026799	H1-neurons	neurons:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30026287-30026337	HIPEpiC	eye:	n/a
2	chr6:30026287-30026337	HCF	heart:	n/a
3	chr6:30026287-30026337	HCM	heart:	n/a
4	chr6:30026287-30026337	HRE	kidney:	n/a
5	chr6:30026287-30026337	HRCEpiC	kidney:	n/a
6	chr6:30026287-30026337	IMR90	lung:	fetal
7	chr6:30026287-30026337	ovcar-3	ovarian:	n/a
8	chr6:30026287-30026337	HRPEpiC	eye:	n/a
9	chr6:30026287-30026337	Caco-2	colon:	n/a
10	chr6:30026287-30026337	BJ	skin:	n/a
11	chr6:30026287-30026337	HNPCEpiC	eye:	n/a
12	chr6:30026287-30026337	NT2-D1	testis:	n/a
13	chr6:30026287-30026337	HepG2	liver:	n/a
14	chr6:30026287-30026337	SKMC	muscle:	n/a
15	chr6:30026287-30026337	HMEC	breast:	n/a
16	chr6:30026287-30026337	PrEC	prostate:	n/a
17	chr6:30026287-30026337	PFSK-1	brain:	n/a
18	chr6:30026287-30026337	Jurkat	blood:	n/a
19	chr6:30026287-30026337	CMK	blood:	n/a
20	chr6:30026287-30026337	PANC-1	pancreas:	n/a
21	chr6:30026287-30026337	SK-N-SH_RA	brain:	n/a
22	chr6:30026287-30026337	NHDF-neo	bronchial:	n/a
23	chr6:30026287-30026337	HL-60	blood:	n/a
24	chr6:30026287-30026337	T-47D	breast:	n/a
25	chr6:30026287-30026337	HPAEpiC	pulmonary alveolar:	n/a
26	chr6:30026287-30026337	GM12892	blood:	n/a
27	chr6:30026287-30026337	ECC-1	luminal epithelium:	n/a
28	chr6:30026287-30026337	AG09319	gingival:	n/a
29	chr6:30026287-30026337	HAEpiC	amniotic membrane:	n/a
30	chr6:30026287-30026337	AoSMC	blood vessel:	n/a
31	chr6:30026287-30026337	NH-A	brain:	n/a
32	chr6:30026287-30026337	SAEC	small airway:	n/a
33	chr6:30026287-30026337	SK-N-SH	brain:	n/a
34	chr6:30026287-30026337	GM19239	blood:	n/a
35	chr6:30026287-30026337	H1-hESC	embryonic stem cell:	embryo
36	chr6:30026287-30026337	Hepatocyte	liver:	n/a
37	chr6:30026287-30026337	NB4	blood:	n/a
38	chr6:30026287-30026337	RPTEC	kidney:	n/a
39	chr6:30026287-30026337	AG04450	lung:	fetal
40	chr6:30026287-30026337	GM12878	blood:	n/a
41	chr6:30026287-30026337	GM12891	blood:	n/a
42	chr6:30026287-30026337	HEEpiC	esophagus:	n/a
43	chr6:30026287-30026337	HCT-116	colon:	n/a
44	chr6:30026287-30026337	NHBE	bronchial:	n/a
45	chr6:30026287-30026337	BE2_C	brain:	n/a
46	chr6:30026287-30026337	K562	blood:	n/a
47	chr6:30026287-30026337	HUVEC	blood vessel:	n/a
48	chr6:30026287-30026337	MCF-7	breast:	n/a
49	chr6:30026287-30026337	AG09309	skin:	n/a
50	chr6:30026287-30026337	U87	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30023200..30024877-chr6:30024886..30026414,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF39-4	chr6:30026145-30026524	ENSG00000204623
2	lnc-RNF39-4	chr6:30026145-30028756	ENSG00000204623

No data

Variant related genes	Relation type
ZNRD1	TF binding region
ZNRD1	CpG island

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs16896044	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16896851	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16896923	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16896970	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17180227	0.91[EUR][1000 genomes]
rs17180836	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17186566	0.91[EUR][1000 genomes]
rs17187693	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17193696	0.95[EUR][1000 genomes]
rs2275854	0.82[ASN][1000 genomes]
rs2286404	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2394249	0.95[EUR][1000 genomes]
rs2893999	0.95[EUR][1000 genomes]
rs3823368	0.95[EUR][1000 genomes]
rs55664658	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55808509	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56073777	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56149225	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56181708	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56185319	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56270681	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289102	0.95[EUR][1000 genomes]
rs56378970	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57969034	0.81[ASN][1000 genomes]
rs58161072	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60774507	0.81[ASN][1000 genomes]
rs62388723	0.90[EUR][1000 genomes]
rs62388749	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62388750	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62388751	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62388752	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62388754	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62388755	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62388756	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62388757	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390160	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390162	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390181	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10484549	HLA-H	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
2	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
3	chr6:29975800-30027800	Weak transcription	Gastric	stomach
4	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
8	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
10	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
11	chr6:29988600-30027400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:29998000-30027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:29999200-30027200	Weak transcription	Fetal Heart	heart
14	chr6:30000000-30027400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:30001200-30027800	Weak transcription	Fetal Kidney	kidney
16	chr6:30003000-30027200	Weak transcription	Dnd41	blood
17	chr6:30006200-30027600	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:30011000-30027800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:30012400-30027400	Weak transcription	HepG2	liver
20	chr6:30012600-30027200	Weak transcription	HMEC	breast
21	chr6:30012600-30027800	Weak transcription	Small Intestine	intestine
22	chr6:30012800-30027600	Weak transcription	NHDF-Ad	bronchial
23	chr6:30012800-30027800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:30012800-30027800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:30013000-30027400	Weak transcription	NHEK	skin
26	chr6:30013000-30027400	Weak transcription	NHLF	lung
27	chr6:30013000-30027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:30013400-30027600	Weak transcription	NH-A	brain
29	chr6:30013600-30027600	Weak transcription	Hela-S3	cervix
30	chr6:30013600-30027800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:30013600-30027800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:30013800-30027200	Weak transcription	GM12878-XiMat	blood
33	chr6:30014000-30028000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:30015600-30027400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:30015600-30027600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:30016000-30027800	Weak transcription	Spleen	Spleen
37	chr6:30016800-30027400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:30017000-30027600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:30017400-30028400	Weak transcription	Lung	lung
40	chr6:30018000-30027600	Weak transcription	Brain Germinal Matrix	brain
41	chr6:30018800-30027200	Weak transcription	Osteobl	bone
42	chr6:30020000-30027800	Weak transcription	Fetal Stomach	stomach
43	chr6:30020200-30027600	Weak transcription	HUVEC	blood vessel
44	chr6:30020200-30027800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:30020400-30028200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr6:30021400-30026400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:30021400-30026600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:30021400-30027400	Weak transcription	A549	lung
49	chr6:30021400-30027600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:30021400-30027800	Weak transcription	Fetal Brain Female	brain

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