Variant report

Variant	rs2301801
Chromosome Location	chr7:106870746-106870747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:106869281..106872161-chr7:106872370..106874834,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12112877	0.87[ASN][1000 genomes]
rs12670688	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12672451	0.90[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13230144	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17153981	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17154040	0.83[ASN][1000 genomes]
rs2107317	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237658	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237659	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237660	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237661	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237662	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237665	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283038	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2395868	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2395869	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34021916	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3801964	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3801966	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4730220	0.82[ASN][1000 genomes]
rs62482493	0.87[ASN][1000 genomes]
rs62482499	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62482502	0.82[ASN][1000 genomes]
rs62482503	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62483619	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62483627	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62483629	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62483633	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62483634	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62483640	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62483641	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6949634	0.83[ASN][1000 genomes]
rs7777950	0.83[ASN][1000 genomes]
rs7785892	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7788271	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7788330	0.82[ASN][1000 genomes]
rs7803151	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs982447	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831087	chr7:106673465-106872460	Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv2756226	chr7:106850755-106944563	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2301801	BCAP29	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106844200-106873200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr7:106844600-106873600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:106844600-106880400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:106844600-106888400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:106846000-106925800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:106849000-106873200	Weak transcription	Brain Anterior Caudate	brain
7	chr7:106849200-106872600	Weak transcription	HSMM	muscle
8	chr7:106850400-106890000	Weak transcription	Hela-S3	cervix
9	chr7:106850800-106871000	Weak transcription	HMEC	breast
10	chr7:106850800-106895200	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:106851000-106873600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:106851000-106897600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr7:106851000-106946000	Weak transcription	Esophagus	oesophagus
14	chr7:106851200-106873200	Weak transcription	Pancreas	Pancrea
15	chr7:106851200-106874800	Weak transcription	Ovary	ovary
16	chr7:106851200-106882200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:106851200-106888200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:106851200-106892400	Weak transcription	Gastric	stomach
19	chr7:106851200-106892600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:106851400-106873200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:106851600-106871400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:106853400-106925600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr7:106854400-106878000	Weak transcription	K562	blood
24	chr7:106855200-106873600	Weak transcription	Right Ventricle	heart
25	chr7:106855600-106883000	Weak transcription	Dnd41	blood
26	chr7:106857200-106877000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:106860200-106882600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:106861400-106873200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:106861600-106876200	Weak transcription	Fetal Brain Female	brain
30	chr7:106863400-106871200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:106863600-106874000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:106863800-106873200	Weak transcription	Psoas Muscle	Psoas
33	chr7:106863800-106873200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr7:106863800-106887400	Weak transcription	Thymus	Thymus
35	chr7:106864000-106875800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:106864000-106878400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:106864000-106889600	Weak transcription	Spleen	Spleen
38	chr7:106864400-106871200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr7:106864400-106871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:106865000-106887000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:106865200-106872800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:106865200-106873600	Weak transcription	Right Atrium	heart
43	chr7:106865200-106884400	Weak transcription	Fetal Muscle Leg	muscle
44	chr7:106865400-106871000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:106865400-106873600	Weak transcription	GM12878-XiMat	blood
46	chr7:106865400-106884400	Weak transcription	Fetal Thymus	thymus
47	chr7:106865600-106871000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr7:106865600-106873200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr7:106865600-106873200	Weak transcription	Left Ventricle	heart
50	chr7:106865600-106873600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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