Variant report

Variant	rs2049500
Chromosome Location	chr3:119216554-119216555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr3:119215802-119218062	GM12878	blood:	n/a	n/a
2	SIN3AK20	chr3:119216517-119217982	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:119215414-119217916	K562	blood:	n/a	n/a
4	MAFK	chr3:119216542-119216854	HepG2	liver:	n/a	n/a
5	GABPA	chr3:119216469-119218222	MCF-7	breast:	n/a	chr3:119217351-119217360
6	POLR2A	chr3:119216045-119217915	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:119216516-119218683	K562	blood:	n/a	n/a
8	POLR2A	chr3:119216039-119216895	U87	brain:	n/a	n/a
9	POLR2A	chr3:119216115-119217972	GM12891	blood:	n/a	n/a
10	POLR2A	chr3:119216492-119218065	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:119216239-119217945	HepG2	liver:	n/a	n/a
12	MXI1	chr3:119216044-119220289	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:119216409-119217948	PBDE	blood:	n/a	n/a
14	POLR2A	chr3:119216528-119217908	HCT-116	colon:	n/a	n/a
15	POLR2A	chr3:119215964-119218008	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr3:119216051-119218651	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:119216376-119217918	U87	brain:	n/a	n/a
18	POLR2A	chr3:119216294-119217975	Hela-S3	cervix:	n/a	n/a
19	GABPA	chr3:119216471-119218033	A549	lung:	n/a	chr3:119217351-119217360
20	POLR2A	chr3:119216286-119217924	K562	blood:	n/a	n/a
21	POLR2A	chr3:119216028-119218789	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:119215989-119217841	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:119215979-119219829	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr3:119216382-119217912	U87	brain:	n/a	n/a
25	POLR2A	chr3:119216074-119217966	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119182024..119184224-chr3:119215586..119219856,7	MCF-7	breast:
2	chr3:118954843..118957176-chr3:119215915..119217953,2	MCF-7	breast:
3	chr3:119216549..119217049-chr8:28243322..28244097,2	Hela-S3	cervix:
4	chr3:119201366..119207142-chr3:119210949..119217240,7	K562	blood:
5	chr3:119185641..119191138-chr3:119214841..119219392,9	MCF-7	breast:
6	chr3:119181870..119185760-chr3:119214240..119218868,7	K562	blood:
7	chr3:119181428..119184178-chr3:119215849..119218868,6	K562	blood:
8	chr3:119186169..119189555-chr3:119214375..119219589,12	K562	blood:
9	chr3:119215767..119217677-chr3:119394561..119396315,2	MCF-7	breast:
10	chr3:119215976..119218932-chr3:119393949..119396539,3	K562	blood:
11	chr3:119186243..119189555-chr3:119215703..119218960,7	K562	blood:
12	chr3:119185037..119191105-chr3:119214944..119221331,23	MCF-7	breast:
13	chr3:119215904..119218714-chr3:135913674..135916504,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD80-3	chr3:119216525-119217028	ENSG00000272662.1

No data

Variant related genes	Relation type
TIMMDC1	TF binding region
ENSG00000186918	Chromatin interaction
ENSG00000138495	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000121578	Chromatin interaction
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11539377	0.83[ASW][hapmap];0.89[YRI][hapmap]
rs11707612	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11709468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714738	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714843	0.92[ASN][1000 genomes]
rs11719448	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11720158	0.91[ASN][1000 genomes]
rs11720423	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11916272	0.83[ASW][hapmap];0.89[YRI][hapmap]
rs11916344	0.83[ASW][hapmap];0.89[YRI][hapmap]
rs11925305	0.89[YRI][hapmap]
rs1599795	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1599796	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs17203104	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs17203188	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1961132	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276713	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2280670	0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2293371	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34090996	0.87[ASN][1000 genomes]
rs3732418	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs3755579	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4447803	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4461452	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687851	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs4687854	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4687863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688002	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap]
rs4688009	0.93[ASN][1000 genomes]
rs4688011	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4688013	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs57506457	0.86[ASN][1000 genomes]
rs59024323	0.93[ASN][1000 genomes]
rs60938951	0.83[ASN][1000 genomes]
rs62263444	0.89[ASN][1000 genomes]
rs62264483	0.91[ASN][1000 genomes]
rs62264487	0.91[ASN][1000 genomes]
rs6438534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775021	0.89[YRI][hapmap]
rs6788474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808654	0.89[YRI][hapmap]
rs7610335	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7642119	0.83[ASW][hapmap];0.89[YRI][hapmap]
rs9289131	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9832341	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850413	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869760	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2049500	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:119189000-119216600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:119196400-119216600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:119196800-119216800	Weak transcription	Small Intestine	intestine
5	chr3:119197400-119216600	Weak transcription	Aorta	Aorta
6	chr3:119205600-119216600	Weak transcription	Colonic Mucosa	Colon
7	chr3:119205600-119216600	Weak transcription	Esophagus	oesophagus
8	chr3:119205600-119216600	Weak transcription	Gastric	stomach
9	chr3:119205800-119216600	Weak transcription	Pancreas	Pancrea
10	chr3:119205800-119217000	Weak transcription	Spleen	Spleen
11	chr3:119206000-119216600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:119207000-119216800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:119207200-119216600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:119207400-119216600	Weak transcription	Ovary	ovary
15	chr3:119207800-119216600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:119208600-119216600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:119209000-119216600	Weak transcription	Fetal Stomach	stomach
18	chr3:119209000-119216600	Weak transcription	Lung	lung
19	chr3:119211000-119216600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:119211400-119216600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:119211600-119216600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:119211800-119216600	Weak transcription	Primary B cells from cord blood	blood
23	chr3:119211800-119216600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:119211800-119216600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:119211800-119216600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:119211800-119216600	Weak transcription	Fetal Brain Female	brain
27	chr3:119211800-119216600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:119211800-119216600	Weak transcription	Fetal Thymus	thymus
29	chr3:119212000-119216600	Weak transcription	Left Ventricle	heart
30	chr3:119212200-119216600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr3:119212200-119216600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:119212200-119216600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:119215800-119216600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:119216000-119216600	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr3:119216000-119216600	Flanking Active TSS	GM12878-XiMat	blood
36	chr3:119216000-119216800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:119216000-119216800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:119216000-119216800	Flanking Active TSS	Fetal Heart	heart
39	chr3:119216000-119216800	Flanking Active TSS	Dnd41	blood
40	chr3:119216000-119217000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:119216000-119218800	Active TSS	NHLF	lung
42	chr3:119216200-119216600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:119216200-119216600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:119216200-119216600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:119216200-119216600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:119216200-119216600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr3:119216200-119216600	Flanking Active TSS	Fetal Lung	lung
48	chr3:119216200-119216600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr3:119216200-119216600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:119216200-119216600	Enhancers	Stomach Mucosa	stomach

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