Variant report

Variant	rs2508657
Chromosome Location	chr11:66043898-66043899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66043747-66044210	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:66043668-66044839	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:66043862-66044168	K562	blood:	n/a	n/a
4	POLR2A	chr11:66043862-66044130	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr11:66043784-66044290	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:66043849-66043988	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:66043616-66044291	K562	blood:	n/a	n/a
8	POLR2A	chr11:66043656-66044275	GM12891	blood:	n/a	n/a
9	POLR2A	chr11:66043884-66044267	GM12891	blood:	n/a	n/a
10	POLR2A	chr11:66041812-66044385	K562	blood:	n/a	n/a
11	POLR2A	chr11:66043553-66044292	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:66042282-66046515	GM12892	blood:	n/a	n/a
13	POLR2A	chr11:66042211-66045771	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:66043669-66046044	GM12892	blood:	n/a	n/a
15	POLR2A	chr11:66043704-66043981	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:66043697-66043926	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227578119..227581046-chr11:66042464..66044320,2	MCF-7	breast:
2	chr11:66023062..66027568-chr11:66043406..66047432,6	MCF-7	breast:
3	chr11:66043530..66045792-chr11:66110035..66112602,2	MCF-7	breast:

No data

Variant related genes	Relation type
CNIH2	TF binding region
ENSG00000174744	Chromatin interaction
ENSG00000174996	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10791865	0.96[ASN][1000 genomes]
rs10896104	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1115508	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151537	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1151539	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1151540	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203798	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1717669	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1892939	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3016319	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs474005	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs521109	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs528842	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555360	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs555853	1.00[ASN][1000 genomes]
rs556595	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs708471	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs708472	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs801731	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs801734	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801735	0.83[EUR][1000 genomes]
rs801736	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801737	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801739	0.89[EUR][1000 genomes]
rs801741	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9326370	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897773	chr11:66041807-66063654	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv555223	chr11:66041807-66064126	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	esv3438726	chr11:66042776-66047874	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv897774	chr11:66042962-66063654	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv897775	chr11:66042962-66064850	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv897776	chr11:66042962-66066349	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2508657	RP11-867G23.1	cis	Muscle Skeletal	GTEx
rs2508657	KLC2	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66037400-66044600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:66037400-66044800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:66037600-66044600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:66037600-66045000	Genic enhancers	Fetal Thymus	thymus
5	chr11:66037800-66044000	Strong transcription	NHEK	skin
6	chr11:66037800-66044200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:66037800-66044600	Strong transcription	Fetal Intestine Small	intestine
8	chr11:66037800-66044800	Strong transcription	Fetal Stomach	stomach
9	chr11:66038000-66044200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr11:66038000-66044200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:66038000-66044200	Strong transcription	Brain Cingulate Gyrus	brain
12	chr11:66038000-66044200	Strong transcription	Fetal Intestine Large	intestine
13	chr11:66038000-66044200	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr11:66038000-66044200	Strong transcription	NHLF	lung
15	chr11:66038000-66044600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:66038000-66044600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:66038000-66044800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:66038200-66044200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:66038200-66044200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr11:66038200-66044200	Strong transcription	Colonic Mucosa	Colon
21	chr11:66038200-66044200	Strong transcription	Lung	lung
22	chr11:66038200-66044200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr11:66038200-66044600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:66038200-66045000	Weak transcription	Right Atrium	heart
25	chr11:66038400-66044000	Strong transcription	Brain Anterior Caudate	brain
26	chr11:66038400-66044400	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr11:66038400-66044800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:66038400-66045000	Weak transcription	Fetal Heart	heart
29	chr11:66038400-66045000	Strong transcription	Gastric	stomach
30	chr11:66038400-66045200	Weak transcription	Psoas Muscle	Psoas
31	chr11:66038600-66044000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr11:66038600-66044000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr11:66038600-66044000	Strong transcription	Placenta	Placenta
34	chr11:66038600-66044000	Strong transcription	Dnd41	blood
35	chr11:66038600-66044400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:66038800-66044200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr11:66038800-66044200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr11:66039000-66044000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:66039000-66044000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:66039200-66044000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:66039200-66044000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:66039200-66044000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:66039200-66044000	Strong transcription	Primary T cells from cord blood	blood
44	chr11:66039200-66044000	Strong transcription	Liver	Liver
45	chr11:66039200-66044000	Strong transcription	Brain Angular Gyrus	brain
46	chr11:66039200-66044200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr11:66039200-66044200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:66039200-66044200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:66039200-66044200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:66039200-66044200	Strong transcription	Brain Germinal Matrix	brain

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