Variant report

Variant	rs1771466
Chromosome Location	chr1:228282175-228282176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228274276-228290284	K562	blood:	n/a	n/a
2	POLR2A	chr1:228282169-228282427	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:228282142-228282492	GM12891	blood:	n/a	n/a
4	TCF12	chr1:228282100-228282700	A549	lung:	n/a	n/a
5	POLR2A	chr1:228282090-228282454	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:228281522-228282637	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:228282066-228282529	K562	blood:	n/a	n/a
8	POLR2A	chr1:228281517-228282740	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr1:228281688-228282423	GM12878	blood:	n/a	n/a
10	CBX3	chr1:228281725-228282732	K562	blood:	n/a	n/a
11	POLR2A	chr1:228281597-228282425	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:228282013-228282426	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
14	KAP1	chr1:228281869-228282834	K562	blood:	n/a	n/a
15	POLR2A	chr1:228282168-228282419	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:228279745-228282720	K562	blood:	n/a	n/a
17	POLR2A	chr1:228281686-228283098	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:228279806-228282603	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:228281416-228282696	K562	blood:	n/a	n/a
20	POLR2A	chr1:228275014-228282866	GM12878	blood:	n/a	n/a
21	KAP1	chr1:228281807-228282875	HEK293	kidney:	n/a	chr1:228282846-228282854
22	POLR2A	chr1:228281659-228282699	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr1:228281481-228282209	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:228281613-228282588	GM12891	blood:	n/a	n/a
25	POLR2A	chr1:228281807-228282819	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:228281554-228282541	GM12891	blood:	n/a	n/a
27	POLR2A	chr1:228281557-228282586	HL-60	blood:	n/a	n/a
28	RFX5	chr1:228282145-228282195	K562	blood:	n/a	n/a
29	POLR2A	chr1:228282124-228282694	K562	blood:	n/a	n/a
30	POLR2A	chr1:228281665-228282637	A549	lung:	n/a	n/a
31	POLR2A	chr1:228281982-228282269	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:228281021..228283258-chr1:228327400..228329608,2	MCF-7	breast:
2	chr1:228280178..228282214-chr1:228355468..228357999,2	K562	blood:
3	chr1:228281446..228284269-chr1:228337109..228339071,2	K562	blood:
4	chr1:228282033..228284613-chr1:228342310..228344410,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3620	TF binding region
ENSG00000198835	Chromatin interaction
ENSG00000143774	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10916269	0.92[ASW][hapmap];1.00[MEX][hapmap]
rs1771454	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1771465	0.87[AMR][1000 genomes]
rs1771475	0.92[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs1934881	0.84[AFR][1000 genomes]
rs1934882	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs2313599	0.81[AFR][1000 genomes]
rs4653535	0.84[AFR][1000 genomes]
rs4653916	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs6667424	0.81[AFR][1000 genomes]
rs6686210	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs7534419	0.81[YRI][hapmap]
rs822728	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs822729	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs822730	0.82[AFR][1000 genomes]
rs822731	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs822732	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822741	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs849750	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs947083	0.84[AFR][1000 genomes]
rs947086	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][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	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1771466	TPBG	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228273000-228284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:228275800-228286600	Weak transcription	Fetal Kidney	kidney
5	chr1:228276600-228285000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:228276800-228290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:228277200-228290000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:228277600-228289200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:228278000-228289400	Genic enhancers	Pancreas	Pancrea
10	chr1:228278400-228282200	Weak transcription	Aorta	Aorta
11	chr1:228278800-228282800	ZNF genes & repeats	GM12878-XiMat	blood
12	chr1:228278800-228283000	ZNF genes & repeats	Dnd41	blood
13	chr1:228278800-228283600	Weak transcription	Ovary	ovary
14	chr1:228279000-228282200	Genic enhancers	Spleen	Spleen
15	chr1:228279000-228285000	Weak transcription	HSMMtube	muscle
16	chr1:228279200-228287800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:228279400-228283400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:228279400-228284200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:228279600-228285600	Weak transcription	NH-A	brain
20	chr1:228279600-228289000	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr1:228279800-228282600	ZNF genes & repeats	K562	blood
22	chr1:228280000-228282200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr1:228280000-228283600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:228280000-228283600	ZNF genes & repeats	Thymus	Thymus
25	chr1:228280000-228284000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:228280000-228284000	ZNF genes & repeats	Fetal Thymus	thymus
27	chr1:228280000-228284200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:228280000-228285200	ZNF genes & repeats	Fetal Stomach	stomach
29	chr1:228280200-228282800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:228280200-228282800	ZNF genes & repeats	HepG2	liver
31	chr1:228280200-228283200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr1:228280200-228283400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
33	chr1:228280200-228284400	ZNF genes & repeats	Fetal Brain Female	brain
34	chr1:228280200-228288800	Weak transcription	Fetal Heart	heart
35	chr1:228280400-228283400	ZNF genes & repeats	A549	lung
36	chr1:228280400-228283600	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr1:228280400-228285400	ZNF genes & repeats	Brain Germinal Matrix	brain
38	chr1:228280600-228282200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:228280600-228282800	Strong transcription	Osteobl	bone
40	chr1:228280600-228283800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:228280600-228286400	Weak transcription	Psoas Muscle	Psoas
42	chr1:228280800-228282400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:228280800-228282800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
44	chr1:228280800-228283400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:228280800-228289600	Weak transcription	Small Intestine	intestine
46	chr1:228281000-228282200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:228281000-228282400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:228281000-228283000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:228281000-228283200	ZNF genes & repeats	Fetal Intestine Large	intestine
50	chr1:228281000-228283400	ZNF genes & repeats	Fetal Muscle Trunk	muscle

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