Variant report

Variant	rs12099145
Chromosome Location	chr11:85338281-85338282
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr11:85338169-85340260	H1-neurons	neurons:	n/a	chr11:85339311-85339324
2	MXI1	chr11:85337986-85341424	SK-N-SH	brain:	n/a	n/a
3	GTF2F1	chr11:85338274-85338734	Hela-S3	cervix:	n/a	n/a
4	NFIC	chr11:85338123-85338731	SK-N-SH	brain:	n/a	n/a
5	SIN3A	chr11:85338244-85340547	H1-hESC	embryonic stem cell:	n/a	chr11:85338982-85338991 chr11:85339543-85339556
6	SMARCC1	chr11:85338279-85340065	Hela-S3	cervix:	n/a	n/a
7	MAZ	chr11:85337895-85340363	IMR90	lung:	n/a	chr11:85339634-85339643 chr11:85339540-85339550
8	POLR2A	chr11:85338230-85340287	H1-hESC	embryonic stem cell:	n/a	n/a
9	HCFC1	chr11:85338075-85341066	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:85338236-85338618	SK-N-SH	brain:	n/a	n/a
11	MXI1	chr11:85338116-85340634	IMR90	lung:	n/a	n/a
12	ZKSCAN1	chr11:85338211-85338446	Hela-S3	cervix:	n/a	n/a
13	SIN3AK20	chr11:85338175-85340321	MCF-7	breast:	n/a	n/a
14	ZNF384	chr11:85338267-85338516	K562	blood:	n/a	n/a
15	NFIC	chr11:85338138-85338704	ECC-1	luminal epithelium:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:85338252-85338302	AG04450	lung:	fetal
2	chr11:85338252-85338302	NT2-D1	testis:	n/a
3	chr11:85338252-85338302	NHDF-neo	bronchial:	n/a
4	chr11:85338252-85338302	PANC-1	pancreas:	n/a
5	chr11:85338252-85338302	MCF-7	breast:	n/a
6	chr11:85338252-85338302	Hela-S3	cervix:	n/a
7	chr11:85338252-85338302	GM12892	blood:	n/a
8	chr11:85338252-85338302	HL-60	blood:	n/a
9	chr11:85338252-85338302	HUVEC	blood vessel:	n/a
10	chr11:85338252-85338302	AoSMC	blood vessel:	n/a
11	chr11:85338252-85338302	HCM	heart:	n/a
12	chr11:85338252-85338302	PFSK-1	brain:	n/a
13	chr11:85338252-85338302	SK-N-SH_RA	brain:	n/a
14	chr11:85338252-85338302	AG10803	skin:	n/a
15	chr11:85338252-85338302	HEK293	kidney:	embryo
16	chr11:85338252-85338302	HCPEpiC	choroid plexus:	n/a
17	chr11:85338252-85338302	RPTEC	kidney:	n/a
18	chr11:85338252-85338302	HCT-116	colon:	n/a
19	chr11:85338252-85338302	BE2_C	brain:	n/a
20	chr11:85338252-85338302	Caco-2	colon:	n/a
21	chr11:85338252-85338302	K562	blood:	n/a
22	chr11:85338252-85338302	PrEC	prostate:	n/a
23	chr11:85338252-85338302	Jurkat	blood:	n/a
24	chr11:85338252-85338302	GM19239	blood:	n/a
25	chr11:85338252-85338302	A549	lung:	n/a
26	chr11:85338252-85338302	NB4	blood:	n/a
27	chr11:85338252-85338302	HIPEpiC	eye:	n/a
28	chr11:85338252-85338302	IMR90	lung:	fetal
29	chr11:85338252-85338302	MCF10A-Er-Src	breast:	n/a
30	chr11:85338252-85338302	AG09319	gingival:	n/a
31	chr11:85338252-85338302	U87	brain:	n/a
32	chr11:85338252-85338302	BJ	skin:	n/a
33	chr11:85338252-85338302	CMK	blood:	n/a
34	chr11:85338252-85338302	H1-hESC	embryonic stem cell:	embryo
35	chr11:85338252-85338302	Hepatocyte	liver:	n/a
36	chr11:85338252-85338302	GM06990	blood:	n/a
37	chr11:85338252-85338302	HRE	kidney:	n/a
38	chr11:85338252-85338302	HepG2	liver:	n/a
39	chr11:85338252-85338302	GM12878	blood:	n/a
40	chr11:85338252-85338302	NH-A	brain:	n/a
41	chr11:85338252-85338302	GM12891	blood:	n/a
42	chr11:85338252-85338302	SK-N-SH	brain:	n/a
43	chr11:85338252-85338302	HRCEpiC	kidney:	n/a
44	chr11:85338252-85338302	HNPCEpiC	eye:	n/a
45	chr11:85338252-85338302	HPAEpiC	pulmonary alveolar:	n/a
46	chr11:85338252-85338302	HRPEpiC	eye:	n/a
47	chr11:85338252-85338302	SAEC	small airway:	n/a
48	chr11:85338252-85338302	SKMC	muscle:	n/a
49	chr11:85338252-85338302	ProgFib	skin:	n/a
50	chr11:85338252-85338302	ECC-1	luminal epithelium:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85335097..85341629-chr11:85372332..85377145,15	MCF-7	breast:
2	chr11:85337127..85343160-chr11:85357064..85364111,20	MCF-7	breast:
3	chr11:85337740..85341959-chr11:85373645..85377756,6	MCF-7	breast:
4	chr11:85337637..85339242-chr11:85365920..85368158,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM126B	TF binding region
TMEM126B	CpG island
ENSG00000137504	Chromatin interaction
ENSG00000171202	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10501593	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17148234	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17148242	0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17148255	0.83[AMR][1000 genomes]
rs17148267	1.00[MEX][hapmap]
rs17148285	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17148301	1.00[MEX][hapmap]
rs17148316	1.00[MEX][hapmap];0.88[YRI][hapmap]
rs17148332	1.00[MEX][hapmap]
rs17148370	1.00[MEX][hapmap]
rs56047795	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56687664	0.85[AMR][1000 genomes]
rs56838978	0.85[AMR][1000 genomes]
rs57309067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57313830	0.85[AMR][1000 genomes]
rs57361884	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60192818	0.85[AMR][1000 genomes]
rs60734322	0.85[AMR][1000 genomes]
rs60865542	0.85[AMR][1000 genomes]
rs61169921	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61180955	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61198962	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61465434	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6592254	0.85[AMR][1000 genomes]
rs6592256	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6592257	0.93[ASW][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs7103387	0.83[AMR][1000 genomes]
rs7116307	1.00[MEX][hapmap]
rs7116532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7116553	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7122987	0.92[YRI][hapmap];0.85[AMR][1000 genomes]
rs744173	1.00[ASW][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes]
rs7938991	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7942218	0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7946793	0.92[YRI][hapmap]
rs7949114	0.85[AMR][1000 genomes]
rs7952219	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv898047	chr11:85180409-85377707	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv898048	chr11:85206156-85404138	Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85336000-85341000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr11:85336200-85339000	Active TSS	Right Atrium	heart
3	chr11:85336200-85340600	Active TSS	Ovary	ovary
4	chr11:85336200-85341400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr11:85336400-85340400	Active TSS	Aorta	Aorta
6	chr11:85337000-85340200	Active TSS	Stomach Smooth Muscle	stomach
7	chr11:85337200-85338400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:85337200-85340800	Active TSS	Right Ventricle	heart
9	chr11:85337200-85341000	Active TSS	NHLF	lung
10	chr11:85337400-85338400	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr11:85337400-85341000	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr11:85337600-85338400	Enhancers	Primary B cells from peripheral blood	blood
13	chr11:85337600-85338400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:85337600-85338800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:85337600-85339000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:85337600-85339600	Active TSS	Brain Germinal Matrix	brain
17	chr11:85337600-85340400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr11:85337600-85340400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:85337600-85340400	Active TSS	Fetal Heart	heart
20	chr11:85337600-85340400	Active TSS	Fetal Kidney	kidney
21	chr11:85337600-85340400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr11:85337600-85340400	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr11:85337600-85340600	Active TSS	H9 Cell Line	embryonic stem cell
24	chr11:85337600-85340800	Active TSS	Colonic Mucosa	Colon
25	chr11:85337600-85341000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:85337800-85338400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:85337800-85338400	Weak transcription	Small Intestine	intestine
28	chr11:85337800-85338600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr11:85337800-85340000	Active TSS	Brain Cingulate Gyrus	brain
30	chr11:85337800-85340000	Active TSS	Fetal Lung	lung
31	chr11:85337800-85340200	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr11:85337800-85340400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:85337800-85340400	Active TSS	Brain Angular Gyrus	brain
34	chr11:85337800-85340400	Active TSS	Colon Smooth Muscle	Colon
35	chr11:85337800-85340400	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr11:85337800-85340600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr11:85337800-85340600	Active TSS	Fetal Stomach	stomach
38	chr11:85337800-85340600	Active TSS	Left Ventricle	heart
39	chr11:85337800-85340600	Active TSS	Psoas Muscle	Psoas
40	chr11:85337800-85340600	Active TSS	NHDF-Ad	bronchial
41	chr11:85337800-85340800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr11:85337800-85341000	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr11:85337800-85341000	Active TSS	H1 Cell Line	embryonic stem cell
44	chr11:85337800-85341000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:85337800-85341200	Active TSS	Rectal Smooth Muscle	rectum
46	chr11:85338000-85338400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:85338000-85338400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr11:85338000-85338400	Flanking Active TSS	A549	lung
49	chr11:85338000-85338600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr11:85338000-85338600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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