Variant report

Variant	rs836177
Chromosome Location	chr12:50491821-50491822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50491781-50492420	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:50491696-50494205	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:50491697-50492176	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:50491784-50492054	K562	blood:	n/a	n/a
5	ZNF263	chr12:50491776-50492131	HEK293-T-REx	kidney:	n/a	n/a
6	POLR2A	chr12:50491770-50492049	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:50491778-50491959	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:50491806-50492249	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:50491763-50492358	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr12:50491711-50492704	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:50491641-50492031	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:50491797-50491885	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
SMARCD1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1044370	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10747570	0.81[AMR][1000 genomes]
rs1862043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1979702	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2178173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2272391	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs2358538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs578470	0.80[EUR][1000 genomes]
rs646782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580729	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs706790	0.80[EUR][1000 genomes]
rs706791	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs706792	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs706793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7136570	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7279	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7297421	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7301740	0.82[ASN][1000 genomes]
rs7302981	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7308356	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7532	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7967705	0.83[AMR][1000 genomes]
rs7967844	0.81[AMR][1000 genomes]
rs7972842	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs835592	0.96[CEU][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap]
rs836170	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836171	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836173	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836174	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836176	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836179	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs836180	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs836181	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs836188	0.80[EUR][1000 genomes]
rs844347	0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.80[EUR][1000 genomes]
rs860698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	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
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs836177	LASS5	cis	parietal	SCAN
rs836177	LASS5	cis	multi-tissue	Pritchard
rs836177	SLC38A1	cis	parietal	SCAN
rs836177	MCRS1	cis	parietal	SCAN
rs836177	LASS5	cis	cerebellum	SCAN
rs836177	TMEM106C	cis	cerebellum	SCAN
rs836177	SNORA2A	cis	parietal	SCAN
rs836177	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50480000-50494800	Strong transcription	Rectal Mucosa Donor 29	rectum
2	chr12:50480000-50496400	Weak transcription	Right Atrium	heart
3	chr12:50480200-50494800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:50480200-50494800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:50480200-50496200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr12:50480200-50496600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:50480200-50496600	Strong transcription	Thymus	Thymus
8	chr12:50480200-50496800	Strong transcription	Fetal Stomach	stomach
9	chr12:50480400-50493800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:50480400-50494400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr12:50480400-50494400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:50480400-50494600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:50480400-50494800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:50480400-50494800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:50480400-50494800	Strong transcription	Fetal Intestine Large	intestine
16	chr12:50480400-50494800	Strong transcription	Placenta	Placenta
17	chr12:50480400-50495600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:50480400-50495800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:50480400-50496000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:50480400-50496200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:50480400-50496200	Strong transcription	A549	lung
22	chr12:50480400-50496600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:50480400-50496600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:50480400-50496600	Strong transcription	Primary T cells from cord blood	blood
25	chr12:50480400-50496600	Strong transcription	Fetal Lung	lung
26	chr12:50480600-50492200	Strong transcription	Primary hematopoietic stem cells	blood
27	chr12:50480600-50493200	Strong transcription	Adipose Nuclei	Adipose
28	chr12:50480600-50493600	Strong transcription	HSMMtube	muscle
29	chr12:50480600-50494000	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr12:50480600-50494600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:50480600-50494600	Strong transcription	Left Ventricle	heart
32	chr12:50480600-50494800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:50480600-50494800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:50480600-50495000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:50480600-50495000	Strong transcription	Spleen	Spleen
36	chr12:50480600-50495400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:50480600-50495800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:50480800-50494800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr12:50480800-50495000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:50480800-50496400	Strong transcription	Fetal Thymus	thymus
41	chr12:50481000-50494400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:50481000-50496000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:50481400-50494000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:50481600-50496800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:50482000-50494600	Strong transcription	Lung	lung
46	chr12:50482000-50495400	Strong transcription	Fetal Muscle Leg	muscle
47	chr12:50482000-50496600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:50482400-50493000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:50482400-50494800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:50482600-50492600	Strong transcription	HSMM	muscle

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