Variant report

Variant	rs10875941
Chromosome Location	chr12:49667921-49667922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:110)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:110 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49666564-49669264	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:49667500-49669360	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr12:49666920-49668981	HL-60	blood:	n/a	n/a
4	POLR2A	chr12:49666418-49669114	K562	blood:	n/a	n/a
5	POLR2A	chr12:49664684-49670620	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr12:49664820-49669295	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr12:49666805-49668971	GM12878	blood:	n/a	n/a
8	GATA3	chr12:49667335-49668769	A549	lung:	n/a	n/a
9	MBD4	chr12:49667714-49668069	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:49666231-49669369	PFSK-1	brain:	n/a	n/a
11	PML	chr12:49667400-49668044	GM12878	blood:	n/a	n/a
12	HEY1	chr12:49665972-49668094	K562	blood:	n/a	n/a
13	BCL3	chr12:49666451-49668725	K562	blood:	n/a	n/a
14	PML	chr12:49666494-49668041	K562	blood:	n/a	n/a
15	POLR2A	chr12:49664774-49669352	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:49657862-49669371	K562	blood:	n/a	n/a
17	POLR2A	chr12:49667564-49668981	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:49667206-49668074	HepG2	liver:	n/a	n/a
19	POLR2A	chr12:49665913-49669127	GM12891	blood:	n/a	n/a
20	POLR2A	chr12:49666495-49668898	K562	blood:	n/a	n/a
21	POLR2A	chr12:49667234-49669281	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr12:49667884-49668052	A549	lung:	n/a	n/a
23	POLR2A	chr12:49666416-49668859	K562	blood:	n/a	n/a
24	PML	chr12:49666402-49668372	K562	blood:	n/a	n/a
25	TEAD4	chr12:49666897-49667972	K562	blood:	n/a	n/a
26	POLR2A	chr12:49664686-49669267	Hela-S3	cervix:	n/a	n/a
27	TEAD4	chr12:49666403-49667983	K562	blood:	n/a	n/a
28	SIX5	chr12:49667072-49668128	A549	lung:	n/a	n/a
29	POLR2A	chr12:49667481-49668064	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:49666991-49669296	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr12:49666483-49669149	A549	lung:	n/a	n/a
32	POLR2A	chr12:49666548-49668971	HepG2	liver:	n/a	n/a
33	HEY1	chr12:49664685-49668312	K562	blood:	n/a	n/a
34	JUND	chr12:49667022-49668754	HCT-116	colon:	n/a	chr12:49668674-49668681
35	SIN3AK20	chr12:49666478-49668137	K562	blood:	n/a	n/a
36	POLR2A	chr12:49666200-49668091	HepG2	liver:	n/a	n/a
37	POLR2A	chr12:49664707-49670365	U87	brain:	n/a	n/a
38	TCF12	chr12:49667682-49668877	A549	lung:	n/a	n/a
39	POLR2A	chr12:49666601-49668005	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:49666201-49669098	HepG2	liver:	n/a	n/a
41	POLR2A	chr12:49666527-49669299	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr12:49667917-49668036	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:49667494-49668079	A549	lung:	n/a	n/a
44	POLR2A	chr12:49667040-49669023	IMR90	lung:	n/a	n/a
45	NFYA	chr12:49667592-49667964	K562	blood:	n/a	n/a
46	CEBPD	chr12:49666588-49668117	K562	blood:	n/a	n/a
47	POLR2A	chr12:49666614-49669055	K562	blood:	n/a	n/a
48	POLR2A	chr12:49666476-49669259	MCF-7	breast:	n/a	n/a
49	POLR2A	chr12:49666509-49670373	U87	brain:	n/a	n/a
50	HEY1	chr12:49667663-49668045	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49667022..49671096-chr12:49685141..49687523,3	K562	blood:
2	chr12:49667825..49672911-chr12:49731373..49736764,7	K562	blood:
3	chr12:49410579..49413468-chr12:49666098..49668038,2	K562	blood:
4	chr12:49667042..49668619-chr12:49959885..49961439,2	MCF-7	breast:
5	chr12:49667402..49669417-chr12:49680548..49682820,2	K562	blood:
6	chr12:49666275..49670972-chr12:49688443..49691988,7	K562	blood:
7	chr12:49667022..49669779-chr12:49685141..49687257,2	K562	blood:
8	chr12:49666353..49668796-chr19:796925..798586,2	K562	blood:
9	chr12:49523127..49526155-chr12:49667398..49671055,3	K562	blood:
10	chr12:49667913..49670211-chr12:49679594..49681611,2	MCF-7	breast:
11	chr12:49665854..49668915-chr12:49685671..49689413,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258232	TF binding region
ENSG00000011304	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000187778	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10875942	0.88[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11168936	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2335232	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335451	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs3847766	0.91[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs3858586	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858587	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7307435	0.95[CEU][hapmap];0.83[YRI][hapmap]
rs7974831	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv976612	chr12:49666119-49668483	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10875941	MCRS1	cis	cerebellum	SCAN
rs10875941	ATF1	cis	cerebellum	SCAN
rs10875941	WNT10B	cis	parietal	SCAN
rs10875941	PRPH	cis	cerebellum	SCAN
rs10875941	LARP4	cis	parietal	SCAN
rs10875941	POU6F1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
2	chr12:49659600-49668600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:49659600-49669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:49659800-49668600	Weak transcription	Right Atrium	heart
6	chr12:49661000-49668000	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr12:49661000-49669800	Strong transcription	Fetal Stomach	stomach
8	chr12:49661600-49668000	Strong transcription	Fetal Thymus	thymus
9	chr12:49661600-49670600	Weak transcription	Psoas Muscle	Psoas
10	chr12:49661800-49668000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:49662000-49668000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:49662000-49668600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:49662200-49668600	Strong transcription	Primary T cells from cord blood	blood
14	chr12:49662600-49668000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:49662600-49668400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr12:49662600-49669000	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:49662800-49673400	Weak transcription	Brain Anterior Caudate	brain
18	chr12:49662800-49673400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:49662800-49673400	Weak transcription	Brain Substantia Nigra	brain
20	chr12:49663000-49668000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr12:49663000-49668000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:49663000-49668200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr12:49663000-49668400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:49663000-49669600	Strong transcription	Thymus	Thymus
25	chr12:49663000-49669800	Strong transcription	Fetal Intestine Small	intestine
26	chr12:49663200-49668000	Strong transcription	Adipose Nuclei	Adipose
27	chr12:49663200-49668000	Strong transcription	Colonic Mucosa	Colon
28	chr12:49663200-49668000	Strong transcription	Placenta	Placenta
29	chr12:49663200-49668200	Strong transcription	Lung	lung
30	chr12:49663200-49668600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:49663200-49668600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:49663200-49669000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:49663200-49669200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr12:49663400-49668000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:49663400-49668000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:49663400-49668000	Strong transcription	HUVEC	blood vessel
37	chr12:49663400-49668200	Strong transcription	HSMMtube	muscle
38	chr12:49663400-49668400	Strong transcription	Gastric	stomach
39	chr12:49663400-49668600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:49663400-49668800	Strong transcription	Spleen	Spleen
41	chr12:49663400-49669800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:49663600-49668000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr12:49663600-49668400	Strong transcription	Aorta	Aorta
44	chr12:49663600-49669000	Strong transcription	Primary B cells from cord blood	blood
45	chr12:49663800-49668000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:49663800-49668000	Strong transcription	Brain Germinal Matrix	brain
47	chr12:49663800-49669200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:49664000-49668800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:49664200-49668400	Strong transcription	NHEK	skin
50	chr12:49664200-49668600	Strong transcription	Muscle Satellite Cultured Cells	--

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