Variant report

Variant	rs1838571
Chromosome Location	chr10:49759708-49759709
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	RAD21	chr10:49759529-49760355	SK-N-SH_RA	brain:	n/a	chr10:49759730-49759749
2	CTCF	chr10:49759690-49759791	Medullo	brain:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
3	CTCF	chr10:49759674-49759765	H1-hESC	embryonic stem cell:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
4	EP300	chr10:49758900-49760644	SK-N-SH	brain:	n/a	chr10:49760537-49760546 chr10:49760441-49760457 chr10:49760610-49760619
5	CTCF	chr10:49759640-49759790	HEK293	kidney:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
6	SMC3	chr10:49759449-49760743	SK-N-SH	brain:	n/a	chr10:49759731-49759745 chr10:49760454-49760464
7	CTCF	chr10:49759701-49759794	K562	blood:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
8	CTCF	chr10:49759640-49759790	NHDF-neo	bronchial:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
9	CTCF	chr10:49759600-49759750	GM12871	blood:	n/a	chr10:49759729-49759747
10	CTCF	chr10:49759454-49760511	A549	lung:	n/a	chr10:49760416-49760429 chr10:49759729-49759747 chr10:49759731-49759752
11	RAD21	chr10:49759618-49760480	IMR90	lung:	n/a	chr10:49759730-49759749 chr10:49760454-49760464
12	CTCF	chr10:49759660-49759810	AG09309	skin:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
13	CTCF	chr10:49759560-49759710	HBMEC	blood vessel:	n/a	n/a
14	CTCF	chr10:49759680-49759830	GM12870	blood:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
15	RAD21	chr10:49759317-49760650	SK-N-SH	brain:	n/a	chr10:49759730-49759749 chr10:49760623-49760632 chr10:49760454-49760464 chr10:49760621-49760631
16	CTCF	chr10:49759660-49759810	WERI-Rb-1	eye:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
17	CTCF	chr10:49759658-49760357	K562	blood:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
18	RAD21	chr10:49759506-49760414	H1-hESC	embryonic stem cell:	n/a	chr10:49759730-49759749
19	CTCF	chr10:49759680-49759814	GM12892	blood:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
20	CTCF	chr10:49758881-49760623	SK-N-SH	brain:	n/a	chr10:49759297-49759305 chr10:49760416-49760429 chr10:49759729-49759747 chr10:49759731-49759752
21	CTCF	chr10:49759600-49759750	HRPEpiC	eye:	n/a	chr10:49759729-49759747
22	CTCF	chr10:49759652-49759763	SK-N-SH_RA	brain:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
23	CTCF	chr10:49759680-49759830	SAEC	small airway:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
24	POLR2A	chr10:49759488-49761085	U87	brain:	n/a	n/a
25	CTCF	chr10:49759640-49759790	BE2_C	brain:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
26	CTCF	chr10:49759675-49760359	MCF-7	breast:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
27	CTCF	chr10:49759620-49759770	AG04449	skin:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
28	RAD21	chr10:49759581-49760367	SK-N-SH_RA	brain:	n/a	chr10:49759730-49759749
29	POLR2A	chr10:49759607-49760632	U87	brain:	n/a	n/a
30	CTCF	chr10:49759643-49760578	HCT-116	colon:	n/a	chr10:49760416-49760429 chr10:49759729-49759747 chr10:49759731-49759752
31	CTCF	chr10:49759620-49759770	HMEC	breast:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
32	CTCF	chr10:49759680-49759830	Hela-S3	cervix:	n/a	chr10:49759729-49759747 chr10:49759731-49759752
33	CTCF	chr10:49759640-49759790	WERI-Rb-1	eye:	n/a	chr10:49759729-49759747 chr10:49759731-49759752

No.	Distal block	Cell Line	Cell type
1	chr10:49755429..49757315-chr10:49758822..49761538,2	K562	blood:
2	chr10:49758981..49760739-chr10:49863487..49865066,35	MCF-7	breast:
3	chr10:49759598..49760543-chr10:49815964..49816843,2	MCF-7	breast:
4	chr10:49759543..49760694-chr10:49857359..49858495,4	MCF-7	breast:
5	chr10:49759591..49760167-chr10:49857265..49858128,2	MCF-7	breast:
6	chr10:49759298..49760794-chr10:49863704..49864896,18	K562	blood:
7	chr10:49759621..49761193-chr10:49762687..49765041,2	MCF-7	breast:
8	chr10:49759388..49761002-chr10:49863863..49865018,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231906	TF binding region
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10491035	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10776622	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10776624	0.81[ASN][1000 genomes]
rs10776625	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10857600	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10857601	1.00[JPT][hapmap]
rs10857603	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11599380	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12570277	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1373791	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1373793	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1373795	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1445150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1838572	0.85[CEU][hapmap]
rs1867588	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2004665	1.00[CHD][hapmap];0.88[GIH][hapmap]
rs4838419	0.81[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap]
rs4838620	0.81[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap]
rs7093632	1.00[CHD][hapmap]
rs747532	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs7911418	0.91[GIH][hapmap]
rs7919520	1.00[CHD][hapmap]
rs935265	0.85[CEU][hapmap]
rs935266	0.85[CEU][hapmap]
rs935267	0.85[CEU][hapmap]
rs935268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935269	0.85[CEU][hapmap]
rs935270	0.82[CEU][hapmap];1.00[CHD][hapmap];0.86[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1838571	SYT15	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49734400-49762400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:49739400-49762400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:49742600-49774800	Weak transcription	Aorta	Aorta
4	chr10:49751200-49771600	Weak transcription	Pancreas	Pancrea
5	chr10:49752200-49760200	Strong transcription	HSMM	muscle
6	chr10:49753000-49760200	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr10:49753200-49760200	Strong transcription	Osteobl	bone
8	chr10:49753400-49764400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr10:49755000-49761800	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:49756000-49760000	Weak transcription	Ovary	ovary
11	chr10:49756200-49759800	Weak transcription	Fetal Lung	lung
12	chr10:49756400-49759800	Weak transcription	Brain Anterior Caudate	brain
13	chr10:49756400-49759800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:49756600-49759800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:49757000-49759800	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:49757200-49760200	Strong transcription	NHDF-Ad	bronchial
17	chr10:49757400-49759800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:49757400-49760400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:49757400-49761600	Enhancers	HUVEC	blood vessel
20	chr10:49757400-49782200	Weak transcription	HSMMtube	muscle
21	chr10:49757800-49759800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:49758200-49762400	Weak transcription	Right Atrium	heart
23	chr10:49758400-49759800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr10:49758400-49762200	Weak transcription	HMEC	breast
25	chr10:49758600-49762000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:49758800-49759800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:49759000-49760800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr10:49759000-49761400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr10:49759200-49760400	Enhancers	Fetal Thymus	thymus
30	chr10:49759200-49761000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:49759200-49761200	Enhancers	Primary B cells from peripheral blood	blood
32	chr10:49759200-49770400	Weak transcription	NH-A	brain
33	chr10:49759400-49760400	Enhancers	Fetal Muscle Leg	muscle
34	chr10:49759400-49763800	Enhancers	Brain Substantia Nigra	brain
35	chr10:49759600-49760000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr10:49759600-49760000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:49759600-49760000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:49759600-49760200	Weak transcription	NHLF	lung
39	chr10:49759600-49760600	Enhancers	Fetal Muscle Trunk	muscle
40	chr10:49759600-49760800	Enhancers	Brain Angular Gyrus	brain
41	chr10:49759600-49761400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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