Variant report

Variant	rs7622994
Chromosome Location	chr3:119023971-119023972
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	chr3:119023465..119026044-chr3:119041239..119043477,3	MCF-7	breast:
2	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10934489	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11914541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918598	0.80[MEX][hapmap]
rs1542233	0.86[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes]
rs2717260	0.82[CEU][hapmap]
rs4687993	0.94[ASW][hapmap];0.94[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56269733	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6438517	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6775982	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6800491	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs724653	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs7620780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623525	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7625392	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7640033	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[TSI][hapmap]
rs7649558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834125	0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7622994	CD86	cis	cerebellum	SCAN
rs7622994	IQCB1	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119014200-119029800	Weak transcription	Gastric	stomach
2	chr3:119014200-119032800	Weak transcription	Pancreas	Pancrea
3	chr3:119015000-119028600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:119015000-119041200	Weak transcription	Aorta	Aorta
5	chr3:119015200-119041000	Weak transcription	Fetal Kidney	kidney
6	chr3:119015800-119024400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:119015800-119024400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:119016000-119035400	Weak transcription	Fetal Brain Male	brain
9	chr3:119016000-119041000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:119016400-119024000	Weak transcription	Small Intestine	intestine
11	chr3:119016400-119040800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:119016400-119041000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:119016600-119024400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:119016600-119025000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:119016800-119024800	Enhancers	Fetal Heart	heart
16	chr3:119017200-119025000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:119017400-119029800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:119017400-119040600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:119017600-119032400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:119018800-119032800	Weak transcription	Thymus	Thymus
21	chr3:119019200-119024800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:119019200-119024800	Genic enhancers	Fetal Stomach	stomach
23	chr3:119019200-119026000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:119019200-119040800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:119019400-119024200	Enhancers	Placenta	Placenta
26	chr3:119019600-119024800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:119020200-119024400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:119020400-119029800	Weak transcription	Colonic Mucosa	Colon
29	chr3:119020400-119040600	Weak transcription	Esophagus	oesophagus
30	chr3:119020800-119030400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:119020800-119032400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:119021000-119027200	Weak transcription	Brain Substantia Nigra	brain
33	chr3:119021000-119030400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:119021000-119032400	Weak transcription	Primary T cells from cord blood	blood
35	chr3:119021200-119041000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:119021200-119041000	Weak transcription	Fetal Thymus	thymus
37	chr3:119021400-119024000	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:119021600-119024200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:119021600-119024200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:119021600-119024800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr3:119021600-119024800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:119021600-119024800	Enhancers	Right Atrium	heart
43	chr3:119021600-119025000	Enhancers	HSMMtube	muscle
44	chr3:119021800-119024200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:119021800-119024400	Genic enhancers	Fetal Muscle Leg	muscle
46	chr3:119022000-119024000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:119022000-119024200	Enhancers	Placenta Amnion	Placenta Amnion
48	chr3:119022000-119024800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:119022000-119025800	Enhancers	NH-A	brain
50	chr3:119022000-119026200	Enhancers	HSMM	muscle

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