Variant report

Variant	rs3850853
Chromosome Location	chr1:45125356-45125357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45123178..45126721-chr1:45185121..45188649,3	MCF-7	breast:
2	chr1:45122556..45125501-chr1:45194476..45198026,4	K562	blood:
3	chr1:45123055..45126216-chr1:45128563..45131707,5	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction
ENSG00000200169	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1051664	0.86[CHB][hapmap];0.82[GIH][hapmap]
rs11211020	0.85[EUR][1000 genomes]
rs11211021	0.83[TSI][hapmap]
rs11581074	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs11582807	0.84[ASN][1000 genomes]
rs11588956	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap]
rs12022097	0.82[ASN][1000 genomes]
rs1963490	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2236219	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap]
rs34948326	0.88[ASN][1000 genomes]
rs4660818	0.96[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs4660821	0.96[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs4660822	0.84[ASN][1000 genomes]
rs6429544	0.93[CHB][hapmap]
rs6667593	0.92[CHB][hapmap]
rs6668870	0.84[ASN][1000 genomes]
rs6683133	0.94[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7538419	0.88[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7539312	0.86[CHB][hapmap]
rs7539607	0.87[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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3850853	DMAP1	cis	parietal	SCAN
rs3850853	AKR1A1	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45099800-45125600	Strong transcription	Lung	lung
2	chr1:45104000-45138200	Weak transcription	Fetal Brain Male	brain
3	chr1:45111200-45128000	Weak transcription	Right Atrium	heart
4	chr1:45113000-45126200	Weak transcription	Small Intestine	intestine
5	chr1:45113200-45125800	Strong transcription	Fetal Stomach	stomach
6	chr1:45114600-45130000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:45115000-45126000	Weak transcription	HMEC	breast
8	chr1:45115200-45137800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:45115600-45125800	Weak transcription	HSMM	muscle
10	chr1:45115800-45138000	Weak transcription	NHDF-Ad	bronchial
11	chr1:45116000-45130000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:45116600-45127600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:45116800-45125800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:45117000-45125600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:45117200-45125800	Weak transcription	Fetal Lung	lung
16	chr1:45117200-45127600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:45117200-45130200	Weak transcription	Primary B cells from cord blood	blood
18	chr1:45117200-45137800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:45117200-45138600	Weak transcription	Aorta	Aorta
20	chr1:45117400-45125800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:45117400-45125800	Weak transcription	HSMMtube	muscle
22	chr1:45117400-45129200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:45117400-45130200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr1:45117400-45130200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:45117400-45130200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:45117400-45138000	Weak transcription	Left Ventricle	heart
27	chr1:45117600-45130200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:45117800-45125600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:45117800-45126000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:45117800-45128000	Weak transcription	Colonic Mucosa	Colon
31	chr1:45118200-45130200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:45118400-45127600	Weak transcription	Thymus	Thymus
33	chr1:45118400-45129400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:45118400-45130000	Weak transcription	GM12878-XiMat	blood
35	chr1:45118400-45130200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:45118600-45125800	Strong transcription	Fetal Intestine Small	intestine
37	chr1:45118600-45126000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:45118600-45138600	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:45119000-45128800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:45119200-45126800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:45119200-45139200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:45119400-45126000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:45119600-45125800	Weak transcription	Stomach Mucosa	stomach
44	chr1:45119800-45138000	Weak transcription	Primary T cells from cord blood	blood
45	chr1:45120200-45129200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:45120400-45130200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:45120600-45125600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:45120600-45125800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:45120600-45125800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:45120600-45126000	Weak transcription	Esophagus	oesophagus

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