Variant report

Variant	rs2523957
Chromosome Location	chr6:29940260-29940261
allele	C/T
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	POLR2A	chr6:29936914-29943239	K562	blood:	n/a	n/a
2	POLR2A	chr6:29938359-29940763	Hela-S3	cervix:	n/a	n/a

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

Extended variants
information (count: 34 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2256539	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256919	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517670	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523948	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2735079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2735080	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs435766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs444252	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2523957	HLA-H	cis	multi-tissue	Pritchard
rs2523957	ZFP57	cis	multi-tissue	Pritchard
rs2523957	HCG4	cis	multi-tissue	Pritchard
rs2523957	BAK1	cis	cerebellum	SCAN
rs2523957	ZKSCAN3	cis	cerebellum	SCAN
rs2523957	ZFP57	cis	lymphoblastoid	seeQTL
rs2523957	HLA-A	cis	multi-tissue	Pritchard
rs2523957	BTN2A1	cis	cerebellum	SCAN
rs2523957	ZNF323	cis	parietal	SCAN
rs2523957	HLA-F	cis	multi-tissue	Pritchard
rs2523957	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs2523957	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs2523957	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29933600-29942400	Weak transcription	Lung	lung
2	chr6:29934400-29944200	Weak transcription	Aorta	Aorta
3	chr6:29934800-29942600	Weak transcription	Brain Substantia Nigra	brain
4	chr6:29935400-29942600	Weak transcription	GM12878-XiMat	blood
5	chr6:29935400-29943400	Weak transcription	Small Intestine	intestine
6	chr6:29935600-29942600	Weak transcription	Brain Anterior Caudate	brain
7	chr6:29935600-29944800	Weak transcription	Dnd41	blood
8	chr6:29935800-29940400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:29935800-29942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:29936000-29942800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:29936200-29940400	Weak transcription	Esophagus	oesophagus
12	chr6:29936200-29942000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:29936200-29942400	Weak transcription	Right Atrium	heart
14	chr6:29936200-29942400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:29936400-29940400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:29936400-29941400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:29936400-29942600	Weak transcription	HepG2	liver
18	chr6:29936400-29943000	Weak transcription	Psoas Muscle	Psoas
19	chr6:29936600-29940400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:29936600-29942200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:29936600-29942400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:29936600-29942800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:29936600-29942800	Weak transcription	HSMMtube	muscle
24	chr6:29936800-29942800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:29937200-29940400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:29937200-29942800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:29937800-29942800	Weak transcription	K562	blood
28	chr6:29938600-29942800	Weak transcription	Colonic Mucosa	Colon
29	chr6:29938800-29940600	Strong transcription	Spleen	Spleen
30	chr6:29939000-29941600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:29939200-29940800	Strong transcription	Fetal Intestine Small	intestine
32	chr6:29939200-29942600	Weak transcription	Adipose Nuclei	Adipose
33	chr6:29939600-29940600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
34	chr6:29939600-29941000	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr6:29939800-29940400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr6:29939800-29940600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:29939800-29940600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:29939800-29940600	Enhancers	Right Ventricle	heart
39	chr6:29939800-29940800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:29939800-29940800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr6:29940000-29940400	Enhancers	Fetal Thymus	thymus
42	chr6:29940000-29940600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:29940000-29940600	Enhancers	Left Ventricle	heart
44	chr6:29940000-29940600	Enhancers	Pancreas	Pancrea
45	chr6:29940000-29940800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:29940000-29940800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr6:29940000-29940800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:29940200-29940600	Strong transcription	Thymus	Thymus
49	chr6:29940200-29940800	Genic enhancers	Gastric	stomach

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