Variant report

Variant	rs6733550
Chromosome Location	chr2:85828014-85828015
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:85825703-85830272	K562	blood:	n/a	n/a
2	POLR2A	chr2:85828007-85830344	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:85825162-85830624	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:85827638-85830320	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:85825892-85830647	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:85826337-85828052	U87	brain:	n/a	n/a
7	POLR2A	chr2:85826219-85830199	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:85827822-85828241	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr2:85827773-85828540	U87	brain:	n/a	n/a
10	POLR2A	chr2:85827789-85828597	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr2:85827564-85828738	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:85828011-85828900	GM12891	blood:	n/a	n/a
13	POLR2A	chr2:85825695-85830271	K562	blood:	n/a	n/a
14	POLR2A	chr2:85827773-85828720	U87	brain:	n/a	n/a
15	POLR2A	chr2:85825540-85828209	K562	blood:	n/a	n/a
16	POLR2A	chr2:85825877-85830216	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:85827869-85828432	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr2:85826366-85828018	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:85825324-85830119	K562	blood:	n/a	n/a
20	POLR2A	chr2:85826331-85828576	U87	brain:	n/a	n/a
21	POLR2A	chr2:85827718-85830692	HUVEC	blood vessel:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
2	chr2:85787126..85789513-chr2:85826931..85829549,2	K562	blood:
3	chr2:85764595..85768669-chr2:85824476..85831716,9	MCF-7	breast:
4	chr2:85784214..85789573-chr2:85827295..85831622,10	MCF-7	breast:
5	chr2:85645470..85649377-chr2:85826700..85831557,5	MCF-7	breast:
6	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
7	chr2:85646032..85649338-chr2:85826916..85831121,5	MCF-7	breast:
8	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
9	chr2:85580316..85583396-chr2:85827550..85830323,4	K562	blood:

No data

Variant related genes	Relation type
TMEM150A	TF binding region
USP39	TF binding region
ENSG00000042493	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000042445	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10180770	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10182351	0.81[JPT][hapmap]
rs10187424	0.80[JPT][hapmap]
rs10198569	0.80[JPT][hapmap]
rs10206961	0.81[GIH][hapmap];0.80[JPT][hapmap]
rs1044158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1078004	0.80[JPT][hapmap]
rs1124836	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs12463933	0.85[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs13383605	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs13406807	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14242	0.81[CHD][hapmap]
rs1562322	0.81[CHD][hapmap]
rs17026396	0.80[JPT][hapmap]
rs2028900	0.80[JPT][hapmap]
rs2040349	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs2044474	0.80[JPT][hapmap]
rs2118177	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs2232745	0.80[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs2232747	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2232748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232750	0.80[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs2304564	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs3755015	0.80[JPT][hapmap]
rs3821020	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs3827550	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs58588820	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62166774	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6547621	0.80[JPT][hapmap]
rs6547629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6643	0.80[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6705971	0.80[JPT][hapmap]
rs6738645	0.80[JPT][hapmap]
rs6743051	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs7568458	0.80[JPT][hapmap]
rs9678632	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9752	0.84[EUR][1000 genomes]

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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6733550	hmm28069	cis	multi-tissue	Pritchard
rs6733550	VAMP8	cis	lymphoblastoid	seeQTL
rs6733550	GGCX	cis	parietal	SCAN
rs6733550	RNF181	cis	brain	BrainEAC
rs6733550	LOC388969	cis	multi-tissue	Pritchard
rs6733550	RNF181	cis	inferior olivary nucleus	BrainEAC
rs6733550	USP39	cis	Heart Left Ventricle	GTEx
rs6733550	GGCX	cis	cerebellum	SCAN
rs6733550	VAMP8	cis	uninvolved skin	skin_eQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85823200-85829200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:85823600-85829000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:85823800-85828800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:85824000-85828200	Genic enhancers	Liver	Liver
5	chr2:85824000-85828400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
6	chr2:85824000-85828600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:85824000-85828600	Genic enhancers	Fetal Intestine Small	intestine
8	chr2:85824000-85828800	Weak transcription	Psoas Muscle	Psoas
9	chr2:85824200-85828200	Strong transcription	Fetal Brain Female	brain
10	chr2:85824200-85828400	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:85824200-85828400	Weak transcription	Right Atrium	heart
12	chr2:85824200-85828600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:85824200-85828600	Genic enhancers	Pancreas	Pancrea
14	chr2:85824400-85828200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:85824400-85828200	Strong transcription	NHLF	lung
16	chr2:85824400-85828400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:85824400-85828400	Strong transcription	Fetal Muscle Leg	muscle
18	chr2:85824400-85828600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:85824400-85828600	Weak transcription	HUVEC	blood vessel
20	chr2:85824400-85829000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:85824600-85828200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:85824600-85828200	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr2:85824600-85828400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:85824600-85828400	Weak transcription	Fetal Brain Male	brain
25	chr2:85824600-85828400	Strong transcription	Fetal Stomach	stomach
26	chr2:85824600-85828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:85824800-85828200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:85824800-85828200	Strong transcription	Spleen	Spleen
29	chr2:85824800-85828400	Weak transcription	NH-A	brain
30	chr2:85824800-85828400	Weak transcription	NHDF-Ad	bronchial
31	chr2:85824800-85828600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:85824800-85828600	Weak transcription	Fetal Heart	heart
33	chr2:85824800-85828600	Weak transcription	Stomach Mucosa	stomach
34	chr2:85825000-85828200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:85825000-85828200	Strong transcription	Thymus	Thymus
36	chr2:85825000-85828600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:85825000-85828600	Weak transcription	HMEC	breast
38	chr2:85825000-85828800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:85825000-85828800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:85825000-85828800	Weak transcription	Fetal Kidney	kidney
41	chr2:85825000-85828800	Weak transcription	Hela-S3	cervix
42	chr2:85825000-85828800	Weak transcription	K562	blood
43	chr2:85825000-85829000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:85825600-85828800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:85825800-85828200	Strong transcription	Ovary	ovary
46	chr2:85825800-85828400	Weak transcription	Primary B cells from cord blood	blood
47	chr2:85825800-85830400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:85826000-85828400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:85826000-85828600	Weak transcription	Colonic Mucosa	Colon
50	chr2:85826000-85828800	Weak transcription	Dnd41	blood

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