Variant report

Variant	rs10506288
Chromosome Location	chr12:50160130-50160131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50159165-50160874	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:50158644-50160717	SK-N-MC	brain:	n/a	n/a
3	FOSL2	chr12:50159185-50160686	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:50159237-50160975	U87	brain:	n/a	n/a
5	POLR2A	chr12:50159488-50160320	MCF-7	breast:	n/a	n/a
6	POLR2A	chr12:50159552-50160484	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:50158621-50160762	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:50159854-50160153	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:50156798-50160681	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:50158475-50160222	K562	blood:	n/a	n/a
11	POLR2A	chr12:50159406-50160757	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:50158680-50160493	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:50159395-50160624	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr12:50159562-50160279	GM12891	blood:	n/a	n/a
15	POLR2A	chr12:50159257-50160303	HCT-116	colon:	n/a	n/a
16	POLR2A	chr12:50158650-50160369	GM12892	blood:	n/a	n/a
17	MTA3	chr12:50159536-50160839	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:50159538-50160208	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr12:50159564-50160805	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr12:50159746-50160279	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr12:50159497-50160949	U87	brain:	n/a	n/a
22	POLR2A	chr12:50158687-50160645	A549	lung:	n/a	n/a
23	POLR2A	chr12:50159244-50160381	HL-60	blood:	n/a	n/a
24	POLR2A	chr12:50158504-50160920	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr12:50159211-50160828	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr12:50159183-50160521	HCT-116	colon:	n/a	n/a
27	POLR2A	chr12:50159536-50160140	ProgFib	skin:	n/a	n/a
28	POLR2A	chr12:50158696-50160931	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr12:50159373-50160753	GM12891	blood:	n/a	n/a
30	POLR2A	chr12:50158516-50160965	PFSK-1	brain:	n/a	n/a
31	BCL3	chr12:50159902-50160974	A549	lung:	n/a	n/a
32	POLR2A	chr12:50158618-50160346	GM12892	blood:	n/a	n/a
33	POLR2A	chr12:50159680-50160711	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr12:50158624-50160342	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr12:50158687-50160665	HepG2	liver:	n/a	n/a
36	NFATC1	chr12:50159350-50160472	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:50158575-50161824	U87	brain:	n/a	n/a
38	POLR2A	chr12:50158581-50161762	U87	brain:	n/a	n/a
39	POLR2A	chr12:50154909-50160837	K562	blood:	n/a	n/a
40	POLR2A	chr12:50159532-50160636	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:50156443..50162111-chr12:50232191..50236705,6	K562	blood:
2	chr12:50145939..50150220-chr12:50153962..50160201,9	K562	blood:
3	chr12:50135671..50138899-chr12:50159080..50162022,3	K562	blood:
4	chr12:50156738..50159324-chr12:50159902..50162287,2	MCF-7	breast:
5	chr12:50143754..50145510-chr12:50159817..50162056,2	MCF-7	breast:
6	chr12:50135904..50138542-chr12:50158281..50161269,2	MCF-7	breast:
7	chr12:50134643..50139812-chr12:50155423..50161657,9	MCF-7	breast:
8	chr12:50159154..50162859-chr12:50163370..50168392,4	MCF-7	breast:
9	chr12:50158953..50161238-chr12:50226769..50228589,2	K562	blood:

No data

Variant related genes	Relation type
LSM6P2	TF binding region
ENSG00000257730	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1012874	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1049986	0.87[CEU][hapmap]
rs10506287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169097	0.87[CEU][hapmap]
rs11169106	0.87[CEU][hapmap]
rs11169125	0.87[CEU][hapmap]
rs11169126	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169127	0.87[CEU][hapmap]
rs11169143	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169145	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830696	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834380	0.87[CEU][hapmap]
rs11836837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299505	0.87[CEU][hapmap]
rs12306422	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306430	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306481	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307828	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310510	0.86[CEU][hapmap]
rs12313353	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12313354	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314795	1.00[CEU][hapmap]
rs12315524	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317778	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1317131	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470906	0.87[CEU][hapmap]
rs1574326	0.87[CEU][hapmap]
rs17123764	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123927	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123970	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993398	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336058	0.87[CEU][hapmap]
rs2336447	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563	0.87[CEU][hapmap]
rs4584654	0.87[CEU][hapmap]
rs4641552	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55637397	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56737983	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56743994	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56906356	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56945609	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57291131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58756176	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59261129	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60094911	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60126713	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60415769	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60613973	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61281663	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137976	0.87[CEU][hapmap]
rs7298080	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74086911	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087113	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087134	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087188	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74089557	0.86[ASN][1000 genomes]
rs74089564	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089566	1.00[ASN][1000 genomes]
rs74089570	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089573	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487779	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7487854	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688	0.87[CEU][hapmap]
rs7952734	0.87[CEU][hapmap]
rs7953412	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964320	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967073	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7968302	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970674	0.87[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971176	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973498	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979262	0.85[CEU][hapmap]
rs9805063	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50146600-50160800	Strong transcription	Fetal Muscle Leg	muscle
2	chr12:50146600-50160800	Strong transcription	Fetal Stomach	stomach
3	chr12:50147200-50160200	Strong transcription	Stomach Smooth Muscle	stomach
4	chr12:50147200-50161000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:50148200-50160200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:50148200-50160200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:50148200-50160200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:50148200-50170000	Weak transcription	Right Atrium	heart
9	chr12:50148400-50160400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:50148800-50160200	Strong transcription	Colon Smooth Muscle	Colon
11	chr12:50155000-50160400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:50156000-50160400	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr12:50158000-50160200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:50158000-50160200	Strong transcription	Adipose Nuclei	Adipose
15	chr12:50158200-50160600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:50158200-50160600	Weak transcription	Small Intestine	intestine
17	chr12:50158200-50161200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:50158200-50162600	Weak transcription	Fetal Heart	heart
19	chr12:50158200-50170200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:50158400-50160200	Weak transcription	Fetal Lung	lung
21	chr12:50158400-50160600	Weak transcription	Ovary	ovary
22	chr12:50158400-50161200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:50158400-50161200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:50158400-50161600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:50158400-50161600	Weak transcription	HUVEC	blood vessel
26	chr12:50158400-50161800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr12:50158400-50161800	Weak transcription	Psoas Muscle	Psoas
28	chr12:50158400-50161800	Weak transcription	Stomach Mucosa	stomach
29	chr12:50158400-50162600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:50158400-50163400	Weak transcription	Spleen	Spleen
31	chr12:50158400-50170000	Weak transcription	Esophagus	oesophagus
32	chr12:50158400-50170200	Weak transcription	A549	lung
33	chr12:50158400-50170200	Weak transcription	K562	blood
34	chr12:50158800-50163800	Weak transcription	GM12878-XiMat	blood
35	chr12:50158800-50170200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr12:50158800-50170400	Weak transcription	Primary B cells from cord blood	blood
37	chr12:50158800-50181600	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:50159000-50160200	Weak transcription	Primary T cells from cord blood	blood
39	chr12:50159000-50160200	Strong transcription	Fetal Thymus	thymus
40	chr12:50159000-50160400	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr12:50159000-50160600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:50159000-50160600	Weak transcription	Brain Angular Gyrus	brain
43	chr12:50159000-50160600	Weak transcription	Colonic Mucosa	Colon
44	chr12:50159000-50160600	Weak transcription	Fetal Kidney	kidney
45	chr12:50159000-50160600	Weak transcription	NHLF	lung
46	chr12:50159000-50160800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:50159000-50161000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:50159000-50161200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:50159000-50161400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:50159000-50161400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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