Variant report

Variant	rs2249059
Chromosome Location	chr6:30656398-30656399
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:30656320-30656470	BJ	skin:	n/a	n/a
2	POLR2A	chr6:30652434-30659300	HUVEC	blood vessel:	n/a	n/a
3	ZNF263	chr6:30653602-30656426	HEK293-T-REx	kidney:	n/a	chr6:30655021-30655042 chr6:30654997-30655018 chr6:30655389-30655398
4	POLR2A	chr6:30653739-30656825	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:30654154-30656479	K562	blood:	n/a	n/a
6	POLR2A	chr6:30653635-30656717	GM12892	blood:	n/a	n/a
7	MTA3	chr6:30652443-30657175	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:30653392-30659188	GM12892	blood:	n/a	n/a
9	POLR2A	chr6:30649497-30657006	HUVEC	blood vessel:	n/a	n/a
10	RUNX3	chr6:30653760-30656478	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:30653817-30656782	GM12892	blood:	n/a	n/a
12	POLR2A	chr6:30655923-30656735	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:30653520-30657649	HUVEC	blood vessel:	n/a	n/a
14	JUN	chr6:30652499-30656649	K562	blood:	n/a	chr6:30655311-30655319
15	POLR2A	chr6:30656194-30656694	K562	blood:	n/a	n/a
16	POLR2A	chr6:30656309-30657512	K562	blood:	n/a	n/a
17	POLR2A	chr6:30653408-30656808	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr6:30656278-30657141	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:30653085-30656801	U87	brain:	n/a	n/a
20	WRNIP1	chr6:30655733-30657165	GM12878	blood:	n/a	n/a
21	PML	chr6:30653377-30656835	GM12878	blood:	n/a	n/a
22	MTA3	chr6:30654606-30656489	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:30649396-30659159	GM12878	blood:	n/a	n/a
24	MXI1	chr6:30652914-30656596	IMR90	lung:	n/a	n/a
25	EBF1	chr6:30656394-30656815	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:30653477-30656921	GM18526	blood:	n/a	n/a
27	POLR2A	chr6:30653755-30659113	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:30653800-30658021	GM19099	blood:	n/a	n/a
29	POLR2A	chr6:30653030-30656860	U87	brain:	n/a	n/a
30	POLR2A	chr6:30656023-30656669	GM12892	blood:	n/a	n/a
31	POLR2A	chr6:30656370-30656863	GM19193	blood:	n/a	n/a
32	POLR2A	chr6:30656373-30657365	Raji	blood:	n/a	n/a
33	POLR2A	chr6:30653184-30656816	GM18951	blood:	n/a	n/a
34	CTCF	chr6:30656380-30656530	GM12866	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:30652587..30660257-chr6:30673612..30681352,12	MCF-7	breast:
2	chr6:30651552..30657864-chr6:30708721..30713716,15	MCF-7	breast:
3	chr6:30521801..30526749-chr6:30651868..30656911,6	K562	blood:
4	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
5	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
6	chr6:30580498..30587281-chr6:30649167..30662031,51	K562	blood:
7	chr6:30655802..30657936-chr6:30780184..30782576,2	K562	blood:
8	chr6:30586081..30587970-chr6:30654610..30657338,2	MCF-7	breast:
9	chr6:30523098..30526363-chr6:30653409..30656727,4	MCF-7	breast:

No data

Variant related genes	Relation type
PPP1R18	TF binding region
ENSG00000137337	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000272273	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17189246	0.83[ASN][1000 genomes]
rs17189399	1.00[AFR][1000 genomes]
rs2239887	0.83[ASN][1000 genomes]
rs2269708	0.83[ASN][1000 genomes]
rs2301277	1.00[AFR][1000 genomes]
rs3778628	1.00[AFR][1000 genomes]
rs41273001	0.83[ASN][1000 genomes]
rs57302671	0.83[ASN][1000 genomes]
rs73422011	0.81[ASN][1000 genomes]
rs73422013	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
6	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
7	nsv884094	chr6:30637998-30660611	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
9	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
10	nsv884095	chr6:30644987-30664567	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv884096	chr6:30647979-30664567	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv884097	chr6:30650378-30660611	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
13	nsv884098	chr6:30650378-30664567	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
14	nsv884099	chr6:30652931-30660611	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2249059	ZNRD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30650800-30656400	Active TSS	Left Ventricle	heart
2	chr6:30653400-30656400	Active TSS	Fetal Kidney	kidney
3	chr6:30654600-30656400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr6:30654800-30656400	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr6:30654800-30656600	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr6:30655000-30658600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:30655000-30659200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr6:30655200-30656400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:30655200-30656400	Flanking Active TSS	Fetal Thymus	thymus
10	chr6:30655200-30656400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr6:30655200-30656600	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr6:30655200-30657200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr6:30655200-30658200	Enhancers	Stomach Mucosa	stomach
14	chr6:30655400-30656400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:30655400-30656400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr6:30655400-30656400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr6:30655400-30656400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr6:30655400-30656400	Flanking Active TSS	HUVEC	blood vessel
19	chr6:30655400-30656400	Flanking Active TSS	Osteobl	bone
20	chr6:30655400-30656600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:30655400-30656600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:30655400-30656800	Flanking Active TSS	HMEC	breast
23	chr6:30655400-30657000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr6:30655400-30658400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:30655600-30656400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:30655600-30656400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr6:30655600-30656400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:30655600-30656400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:30655600-30656400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:30655600-30656600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr6:30655600-30657200	Flanking Active TSS	NHEK	skin
32	chr6:30655600-30658200	Flanking Active TSS	GM12878-XiMat	blood
33	chr6:30655600-30658400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:30655800-30656400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:30655800-30656400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
36	chr6:30655800-30656400	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
37	chr6:30655800-30656400	Transcr. at gene 5' and 3'	Dnd41	blood
38	chr6:30655800-30656600	Enhancers	Brain Hippocampus Middle	brain
39	chr6:30655800-30656600	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr6:30655800-30656600	Flanking Active TSS	Spleen	Spleen
41	chr6:30655800-30656600	Flanking Active TSS	Hela-S3	cervix
42	chr6:30655800-30656600	Flanking Active TSS	NHDF-Ad	bronchial
43	chr6:30655800-30656800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:30655800-30656800	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr6:30655800-30656800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr6:30655800-30656800	Flanking Active TSS	HSMMtube	muscle
47	chr6:30655800-30657000	Transcr. at gene 5' and 3'	NHLF	lung
48	chr6:30655800-30657200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr6:30655800-30657200	Flanking Active TSS	HSMM	muscle
50	chr6:30655800-30657600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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