Variant report

Variant	rs2523943
Chromosome Location	chr6:29942927-29942928
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr6:29942558-29943168	H1-hESC	embryonic stem cell:	n/a	chr6:29942794-29942813
2	MAX	chr6:29942917-29943629	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr6:29942686-29943660	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:29936914-29943239	K562	blood:	n/a	n/a
5	TBP	chr6:29942741-29943001	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:29942906-29942928	K562	blood:	n/a	n/a
7	E2F6	chr6:29942891-29943637	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:29942912-29942982	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr6:29942645-29943161	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr6:29942882-29943628	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HLA-A-1	chr6:29942889-29943294	ENSG00000204625
2	lnc-HLA-A-1	chr6:29942892-29943294	NR_028032

Variant related genes	Relation type
HCG9	TF binding region
MICD	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1128306	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17180241	0.86[ASN][1000 genomes]
rs2232238	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2256820	0.89[ASN][1000 genomes]
rs2256902	0.86[ASN][1000 genomes]
rs2517673	0.94[ASN][1000 genomes]
rs2517676	0.86[ASN][1000 genomes]
rs2517677	0.83[ASN][1000 genomes]
rs2517679	0.81[ASN][1000 genomes]
rs2517680	0.81[ASN][1000 genomes]
rs2517682	0.81[ASN][1000 genomes]
rs2523947	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2523961	0.86[ASN][1000 genomes]
rs2523967	0.89[ASN][1000 genomes]
rs2523969	0.88[ASN][1000 genomes]
rs2524005	0.87[JPT][hapmap]
rs2571404	0.81[ASN][1000 genomes]
rs400488	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs422640	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs453375	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	esv1845786	chr6:29817123-29955129	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv1848127	chr6:29817323-29966451	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	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
11	esv3369212	chr6:29827361-29960177	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	esv32544	chr6:29831716-29944103	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
13	esv2757159	chr6:29834472-29965501	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	esv3376588	chr6:29834667-29964324	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	nsv10810	chr6:29837465-29961415	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
16	nsv870444	chr6:29842885-29949545	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
17	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
18	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
20	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
22	nsv984584	chr6:29932342-29943951	Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	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
24	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
25	esv1799283	chr6:29938777-29959935	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
26	esv3350882	chr6:29942373-29945471	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2523943	ZNRD1	cis	multi-tissue	Pritchard
rs2523943	ZNRD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29934400-29944200	Weak transcription	Aorta	Aorta
2	chr6:29935400-29943400	Weak transcription	Small Intestine	intestine
3	chr6:29935600-29944800	Weak transcription	Dnd41	blood
4	chr6:29936400-29943000	Weak transcription	Psoas Muscle	Psoas
5	chr6:29941600-29944400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:29941800-29943200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr6:29942200-29943400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
8	chr6:29942200-29943400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
9	chr6:29942400-29943000	Enhancers	Gastric	stomach
10	chr6:29942400-29943000	Enhancers	Lung	lung
11	chr6:29942400-29943000	Enhancers	Right Atrium	heart
12	chr6:29942400-29943000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
13	chr6:29942400-29943600	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr6:29942400-29943600	Flanking Active TSS	Spleen	Spleen
15	chr6:29942600-29943000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr6:29942600-29943000	Active TSS	Brain Anterior Caudate	brain
17	chr6:29942600-29943000	Enhancers	Brain Substantia Nigra	brain
18	chr6:29942600-29943000	Enhancers	HepG2	liver
19	chr6:29942600-29943200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:29942600-29943200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
21	chr6:29942600-29943200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr6:29942600-29943200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr6:29942600-29943200	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr6:29942600-29943200	Active TSS	Rectal Smooth Muscle	rectum
25	chr6:29942600-29943400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr6:29942600-29943600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
27	chr6:29942600-29943600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:29942600-29944200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
29	chr6:29942600-29944400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
30	chr6:29942600-29944400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr6:29942600-29944400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
32	chr6:29942600-29945200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr6:29942600-29945400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
34	chr6:29942600-29945400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:29942800-29943000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
36	chr6:29942800-29943000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
37	chr6:29942800-29943000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr6:29942800-29943000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
39	chr6:29942800-29943000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:29942800-29943000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:29942800-29943000	Bivalent Enhancer	Brain Angular Gyrus	brain
42	chr6:29942800-29943000	Active TSS	Brain Hippocampus Middle	brain
43	chr6:29942800-29943000	Flanking Active TSS	Colonic Mucosa	Colon
44	chr6:29942800-29943000	Enhancers	Colon Smooth Muscle	Colon
45	chr6:29942800-29943000	Bivalent Enhancer	Esophagus	oesophagus
46	chr6:29942800-29943000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
47	chr6:29942800-29943000	Active TSS	Stomach Smooth Muscle	stomach
48	chr6:29942800-29943000	Enhancers	K562	blood
49	chr6:29942800-29943200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:29942800-29943200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain

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