Variant report

Variant	rs3828057
Chromosome Location	chr1:151780177-151780178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:151763491..151766160-chr1:151779828..151782203,2	MCF-7	breast:
2	chr1:151777741..151780007-chr1:151780011..151781541,2	MCF-7	breast:
3	chr1:151752426..151754254-chr1:151778758..151780979,2	K562	blood:
4	chr1:151779245..151781251-chr1:151789971..151792071,2	K562	blood:
5	chr1:151774351..151777755-chr1:151779800..151782368,3	K562	blood:
6	chr1:151761843..151763864-chr1:151779499..151782273,2	MCF-7	breast:
7	chr1:151779508..151782077-chr1:151785257..151787936,2	K562	blood:
8	chr1:151779253..151781376-chr1:151783822..151786859,3	MCF-7	breast:
9	chr1:151779832..151781359-chr1:151797431..151800112,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213171	Chromatin interaction
ENSG00000182134	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000143365	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1054475	0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs1123855	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs11806815	0.89[ASN][1000 genomes]
rs12143606	0.83[CHB][hapmap]
rs12748967	0.89[ASN][1000 genomes]
rs12756855	0.89[ASN][1000 genomes]
rs12758387	0.85[CHB][hapmap]
rs1623480	0.85[ASN][1000 genomes]
rs1781420	0.89[ASN][1000 genomes]
rs1781421	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs1781423	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs1781424	0.85[ASN][1000 genomes]
rs1915544	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1996729	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs1996731	0.94[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs1996732	0.85[ASN][1000 genomes]
rs2460997	0.86[ASN][1000 genomes]
rs2495396	0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs35077383	0.84[ASN][1000 genomes]
rs35834074	0.89[ASN][1000 genomes]
rs4240870	0.89[ASN][1000 genomes]
rs4484926	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs4634911	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs4845339	0.88[CHB][hapmap]
rs4845355	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4995159	0.84[ASN][1000 genomes]
rs55982513	0.89[ASN][1000 genomes]
rs60136317	0.94[ASN][1000 genomes]
rs61815091	0.88[ASN][1000 genomes]
rs61815098	0.89[ASN][1000 genomes]
rs61815099	0.89[ASN][1000 genomes]
rs6587619	0.98[ASN][1000 genomes]
rs6672920	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs6680404	0.89[ASN][1000 genomes]
rs6684101	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs7521817	0.86[ASN][1000 genomes]
rs7529549	0.87[ASN][1000 genomes]
rs868866	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs868867	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[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	nsv1010398	chr1:151761649-151790940	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3828057	LYSMD1	cis	cerebellum	SCAN
rs3828057	BCL9	cis	cerebellum	SCAN
rs3828057	CDC42SE1	cis	parietal	SCAN
rs3828057	LCE2C	cis	parietal	SCAN
rs3828057	TDRKH	cis	cerebellum	SCAN
rs3828057	CTSK	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151764200-151787000	Weak transcription	Right Ventricle	heart
2	chr1:151764200-151792800	Weak transcription	Lung	lung
3	chr1:151764600-151782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:151764600-151787600	Weak transcription	Primary T cells from cord blood	blood
5	chr1:151765400-151784200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:151766000-151780200	Weak transcription	Dnd41	blood
7	chr1:151770800-151787200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:151773200-151784800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:151773400-151784800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:151773400-151785000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:151774600-151787000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:151775800-151783600	Weak transcription	Psoas Muscle	Psoas
13	chr1:151776600-151787200	Weak transcription	Spleen	Spleen
14	chr1:151777800-151780200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:151778000-151781800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:151778400-151786000	Strong transcription	Thymus	Thymus
17	chr1:151778400-151792800	Weak transcription	Left Ventricle	heart
18	chr1:151778600-151792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:151778600-151802400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:151778800-151782600	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:151778800-151789200	Weak transcription	Fetal Intestine Small	intestine
22	chr1:151779000-151780200	Strong transcription	Fetal Thymus	thymus
23	chr1:151779000-151781600	Strong transcription	Pancreas	Pancrea
24	chr1:151779000-151787000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:151779200-151783800	Strong transcription	Liver	Liver
26	chr1:151779400-151780800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:151779400-151781200	Enhancers	Brain Substantia Nigra	brain
28	chr1:151779400-151783000	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:151779400-151784200	Enhancers	Brain Hippocampus Middle	brain
30	chr1:151779600-151780200	Strong transcription	Gastric	stomach
31	chr1:151779600-151780800	Enhancers	Brain Germinal Matrix	brain
32	chr1:151779600-151781200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr1:151779800-151780800	Enhancers	Brain Angular Gyrus	brain
34	chr1:151779800-151780800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:151779800-151781800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:151780000-151780800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:151780000-151793400	Weak transcription	Stomach Mucosa	stomach

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