Variant report

Variant	rs259921
Chromosome Location	chr6:29995460-29995461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29995441-29995491	GM12878	blood:	n/a
2	chr6:29995441-29995491	AG09309	skin:	n/a
3	chr6:29995441-29995491	MCF10A-Er-Src	breast:	n/a
4	chr6:29995441-29995491	ovcar-3	ovarian:	n/a
5	chr6:29995441-29995491	BE2_C	brain:	n/a
6	chr6:29995441-29995491	SK-N-SH_RA	brain:	n/a
7	chr6:29995441-29995491	GM12891	blood:	n/a
8	chr6:29995441-29995491	HRPEpiC	eye:	n/a
9	chr6:29995441-29995491	HPAEpiC	pulmonary alveolar:	n/a
10	chr6:29995441-29995491	HUVEC	blood vessel:	n/a
11	chr6:29995441-29995491	RPTEC	kidney:	n/a
12	chr6:29995441-29995491	PANC-1	pancreas:	n/a
13	chr6:29995441-29995491	AoSMC	blood vessel:	n/a
14	chr6:29995441-29995491	AG09319	gingival:	n/a
15	chr6:29995441-29995491	SK-N-MC	brain:	n/a
16	chr6:29995441-29995491	U87	brain:	n/a
17	chr6:29995441-29995491	NT2-D1	testis:	n/a
18	chr6:29995441-29995491	SK-N-SH	brain:	n/a
19	chr6:29995441-29995491	HL-60	blood:	n/a
20	chr6:29995441-29995491	Caco-2	colon:	n/a
21	chr6:29995441-29995491	Hela-S3	cervix:	n/a
22	chr6:29995441-29995491	Jurkat	blood:	n/a
23	chr6:29995441-29995491	SAEC	small airway:	n/a
24	chr6:29995441-29995491	AG04450	lung:	fetal
25	chr6:29995441-29995491	HRE	kidney:	n/a
26	chr6:29995441-29995491	GM12892	blood:	n/a
27	chr6:29995441-29995491	A549	lung:	n/a
28	chr6:29995441-29995491	HCPEpiC	choroid plexus:	n/a
29	chr6:29995441-29995491	HCT-116	colon:	n/a
30	chr6:29995441-29995491	Hepatocyte	liver:	n/a
31	chr6:29995441-29995491	AG04449	skin:	fetal
32	chr6:29995441-29995491	HCF	heart:	n/a
33	chr6:29995441-29995491	HNPCEpiC	eye:	n/a
34	chr6:29995441-29995491	H1-hESC	embryonic stem cell:	embryo
35	chr6:29995441-29995491	BJ	skin:	n/a
36	chr6:29995441-29995491	HEEpiC	esophagus:	n/a
37	chr6:29995441-29995491	HMEC	breast:	n/a
38	chr6:29995441-29995491	HAEpiC	amniotic membrane:	n/a
39	chr6:29995441-29995491	IMR90	lung:	fetal
40	chr6:29995441-29995491	NHDF-neo	bronchial:	n/a
41	chr6:29995441-29995491	GM06990	blood:	n/a
42	chr6:29995441-29995491	HIPEpiC	eye:	n/a
43	chr6:29995441-29995491	PFSK-1	brain:	n/a
44	chr6:29995441-29995491	PrEC	prostate:	n/a
45	chr6:29995441-29995491	AG10803	skin:	n/a
46	chr6:29995441-29995491	CMK	blood:	n/a
47	chr6:29995441-29995491	MCF-7	breast:	n/a
48	chr6:29995441-29995491	HRCEpiC	kidney:	n/a
49	chr6:29995441-29995491	LNCaP	prostate:	n/a
50	chr6:29995441-29995491	NH-A	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29992994..29995481-chr6:29997109..29999804,2	K562	blood:

No data

Variant related genes	Relation type
ETF1P1	CpG island
ENSG00000232757	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1150736	0.86[ASN][1000 genomes]
rs1150741	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150742	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150743	0.94[ASN][1000 genomes]
rs1245371	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1245503	0.92[ASN][1000 genomes]
rs1960063	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2246555	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252965	0.81[EUR][1000 genomes]
rs2256922	0.84[EUR][1000 genomes]
rs2517669	0.83[EUR][1000 genomes]
rs2517672	0.83[EUR][1000 genomes]
rs2523933	0.81[EUR][1000 genomes]
rs2523958	0.82[EUR][1000 genomes]
rs2523959	0.83[EUR][1000 genomes]
rs2523960	0.83[EUR][1000 genomes]
rs2523962	0.83[EUR][1000 genomes]
rs2523963	0.83[EUR][1000 genomes]
rs2523964	0.83[EUR][1000 genomes]
rs2523965	0.83[EUR][1000 genomes]
rs2523971	0.91[EUR][1000 genomes]
rs2530388	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2571376	0.84[EUR][1000 genomes]
rs2571377	0.83[EUR][1000 genomes]
rs259919	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs259923	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259931	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs259933	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259938	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259939	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259943	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2735064	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2735066	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735067	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2735078	0.84[EUR][1000 genomes]
rs2735086	0.81[EUR][1000 genomes]
rs2844805	0.81[EUR][1000 genomes]
rs356954	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs356961	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356966	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356967	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356968	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356969	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs401618	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs426483	0.85[EUR][1000 genomes]
rs9260910	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv969374	chr6:29992833-30001543	Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs259921	ZNRD1	Cis_1M	lymphoblastoid	RTeQTL
rs259921	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs259921	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29974800-30002400	Weak transcription	Dnd41	blood
2	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
3	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
4	chr6:29975800-30027800	Weak transcription	Gastric	stomach
5	chr6:29976200-30001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:29976600-30023000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:29976800-30000800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:29977000-30002000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:29977000-30002000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:29977200-30000400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:29977200-30003800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:29977200-30024600	Weak transcription	Brain Anterior Caudate	brain
13	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
15	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:29979400-30024600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:29979600-30022800	Weak transcription	Ovary	ovary
18	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
19	chr6:29980200-30012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:29981200-30023000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:29981800-30010600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:29982800-30009800	Weak transcription	Psoas Muscle	Psoas
23	chr6:29982800-30022800	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:29983400-30012400	Weak transcription	NHEK	skin
25	chr6:29984600-30023400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:29985000-30024600	Weak transcription	Brain Angular Gyrus	brain
27	chr6:29985400-30008200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:29987400-30001600	Weak transcription	Primary B cells from cord blood	blood
29	chr6:29987800-29996000	Weak transcription	Lung	lung
30	chr6:29987800-30010600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:29987800-30024800	Weak transcription	Fetal Intestine Large	intestine
32	chr6:29988000-30010400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr6:29988200-30000600	Weak transcription	Brain Substantia Nigra	brain
34	chr6:29988200-30000800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:29988200-30009800	Weak transcription	HepG2	liver
36	chr6:29988200-30022800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
39	chr6:29988400-30001200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:29988400-30006200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:29988400-30021600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:29988400-30023400	Weak transcription	Adipose Nuclei	Adipose
43	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
44	chr6:29988600-30003800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:29988600-30009800	Weak transcription	Left Ventricle	heart
46	chr6:29988600-30022200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:29988600-30027400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr6:29988800-29997600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:29988800-30001800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr6:29988800-30001800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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