Variant report

Variant	rs2098839
Chromosome Location	chr11:10676987-10676988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
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	EBF1	chr11:10676691-10677116	GM12878	blood:	n/a	n/a
2	RUNX3	chr11:10676734-10677221	GM12878	blood:	n/a	n/a
3	SP1	chr11:10675687-10677428	HCT-116	colon:	n/a	n/a
4	NR3C1	chr11:10676968-10677155	A549	lung:	n/a	n/a
5	SPI1	chr11:10676540-10677224	HL-60	blood:	n/a	n/a
6	RAD21	chr11:10675532-10677194	HCT-116	colon:	n/a	chr11:10676007-10676026 chr11:10676363-10676370
7	SPI1	chr11:10676746-10677031	GM12891	blood:	n/a	n/a
8	SPI1	chr11:10676678-10677097	HL-60	blood:	n/a	n/a
9	RCOR1	chr11:10676392-10678421	IMR90	lung:	n/a	n/a
10	SP1	chr11:10675697-10677347	HCT-116	colon:	n/a	n/a
11	NR3C1	chr11:10676905-10677256	A549	lung:	n/a	n/a
12	SPI1	chr11:10676793-10677008	GM12878	blood:	n/a	n/a
13	SPI1	chr11:10676786-10677012	K562	blood:	n/a	n/a
14	TCF7L2	chr11:10676828-10677246	HCT-116	colon:	n/a	n/a
15	SPI1	chr11:10676698-10677022	GM12891	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:10584920..10587068-chr11:10674559..10677361,2	K562	blood:
2	chr11:10665821..10668759-chr11:10676865..10679050,3	K562	blood:
3	chr11:10675148..10677906-chr11:10678421..10681418,4	MCF-7	breast:
4	chr11:10534042..10535923-chr11:10675097..10677538,2	MCF-7	breast:
5	chr11:10560102..10563921-chr11:10672313..10677222,4	MCF-7	breast:
6	chr11:10674925..10678334-chr11:10679453..10682484,4	MCF-7	breast:

No data

Variant related genes	Relation type
MRVI1	TF binding region
ENSG00000110315	Chromatin interaction
ENSG00000177112	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1035691	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10840453	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10840457	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042902	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs11042906	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11603178	1.00[JPT][hapmap]
rs1462940	1.00[JPT][hapmap]
rs1544861	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16908001	1.00[JPT][hapmap]
rs16927077	1.00[JPT][hapmap]
rs17318955	1.00[JPT][hapmap]
rs17403439	1.00[JPT][hapmap]
rs17403460	1.00[JPT][hapmap]
rs17403795	1.00[JPT][hapmap]
rs17403942	1.00[JPT][hapmap]
rs17403977	1.00[JPT][hapmap]
rs1863243	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863244	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1979367	1.00[JPT][hapmap]
rs2052690	0.90[AMR][1000 genomes]
rs2052691	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2052692	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4025	1.00[JPT][hapmap]
rs41464450	1.00[JPT][hapmap]
rs4442541	1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4909945	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910160	1.00[JPT][hapmap]
rs4910165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484437	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936275	0.84[AMR][1000 genomes]
rs7940646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881869	1.00[JPT][hapmap]
rs903822	1.00[JPT][hapmap]
rs903823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2098839	TMEM5	trans	cerebellum	SCAN
rs2098839	STK33	cis	parietal	SCAN
rs2098839	SPON1	cis	cerebellum	SCAN
rs2098839	USP47	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10646000-10679000	Weak transcription	Fetal Lung	lung
2	chr11:10646200-10679200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:10650400-10678600	Weak transcription	Right Ventricle	heart
4	chr11:10664200-10678800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:10671400-10677000	Weak transcription	Fetal Intestine Small	intestine
6	chr11:10672000-10679200	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr11:10673000-10682200	Enhancers	Placenta	Placenta
8	chr11:10673200-10677800	Enhancers	Colon Smooth Muscle	Colon
9	chr11:10673400-10679200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr11:10673400-10682800	Enhancers	Ovary	ovary
11	chr11:10673600-10678400	Weak transcription	Left Ventricle	heart
12	chr11:10673600-10678400	Weak transcription	Right Atrium	heart
13	chr11:10673800-10678800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:10673800-10679200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr11:10673800-10681400	Weak transcription	Pancreas	Pancrea
16	chr11:10674000-10677200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:10674000-10677400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:10674000-10681400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:10674200-10681800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr11:10674400-10678000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr11:10674400-10681400	Enhancers	Fetal Muscle Leg	muscle
22	chr11:10674400-10681800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr11:10674600-10678400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:10674600-10678400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:10674600-10689600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:10674800-10677000	Weak transcription	Colonic Mucosa	Colon
27	chr11:10674800-10678800	Enhancers	Rectal Smooth Muscle	rectum
28	chr11:10675000-10678800	Enhancers	K562	blood
29	chr11:10675200-10677600	Enhancers	Primary B cells from cord blood	blood
30	chr11:10675200-10677800	Enhancers	Stomach Smooth Muscle	stomach
31	chr11:10675200-10679000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:10675400-10678600	Enhancers	GM12878-XiMat	blood
33	chr11:10675400-10678800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:10675600-10677200	Enhancers	HMEC	breast
35	chr11:10675600-10677400	Genic enhancers	Aorta	Aorta
36	chr11:10675600-10677400	Weak transcription	Fetal Thymus	thymus
37	chr11:10675600-10677400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr11:10675600-10677600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:10675600-10677800	Enhancers	Adipose Nuclei	Adipose
40	chr11:10675600-10678800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:10675800-10677000	Weak transcription	Lung	lung
42	chr11:10675800-10677000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr11:10675800-10677200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:10675800-10677400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr11:10675800-10678400	Weak transcription	Esophagus	oesophagus
46	chr11:10675800-10678800	Weak transcription	Stomach Mucosa	stomach
47	chr11:10675800-10680000	Weak transcription	Brain Angular Gyrus	brain
48	chr11:10676000-10677200	Enhancers	NHLF	lung
49	chr11:10676000-10677600	Enhancers	NHEK	skin
50	chr11:10676000-10677800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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