Variant report

Variant	rs2576052
Chromosome Location	chr18:44690107-44690108
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	chr18:44687665..44690240-chr18:44700822..44702824,2	MCF-7	breast:
2	chr18:44675461..44681646-chr18:44682135..44691602,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134049	Chromatin interaction
ENSG00000267228	Chromatin interaction
ENSG00000167220	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12953864	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12968552	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13381713	0.87[CEU][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1434529	0.90[EUR][1000 genomes]
rs16954921	0.88[CEU][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16954999	0.92[CEU][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1836259	0.90[EUR][1000 genomes]
rs2289133	0.92[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2317324	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2571002	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2571004	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2571005	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2571006	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2571007	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2571008	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2571010	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2571014	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2571017	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2576057	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2576058	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2635051	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2635052	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2635054	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2635056	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2668758	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2668759	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2668761	0.92[CEU][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2668762	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2668763	0.86[EUR][1000 genomes]
rs2668776	0.83[ASN][1000 genomes]
rs2668777	0.85[ASN][1000 genomes]
rs2668784	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2684819	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2684833	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2684851	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28718304	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4986228	0.84[CEU][hapmap]
rs55730206	0.86[EUR][1000 genomes]
rs7239323	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8085634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8091902	0.85[ASN][1000 genomes]
rs938134	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9953157	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9956809	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9961383	0.92[CEU][hapmap];0.86[EUR][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	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909613	chr18:44644530-44690107	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3412252	chr18:44684003-44711534	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2576052	HDHD2	cis	Muscle Skeletal	GTEx
rs2576052	IER3IP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44677600-44700200	Weak transcription	Aorta	Aorta
2	chr18:44677800-44693400	Weak transcription	Gastric	stomach
3	chr18:44677800-44698200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr18:44677800-44699000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr18:44677800-44700400	Weak transcription	Spleen	Spleen
6	chr18:44677800-44701000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:44677800-44701000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr18:44677800-44701000	Weak transcription	A549	lung
9	chr18:44677800-44701800	Weak transcription	Esophagus	oesophagus
10	chr18:44678000-44699600	Weak transcription	Colon Smooth Muscle	Colon
11	chr18:44678000-44700400	Weak transcription	Small Intestine	intestine
12	chr18:44678000-44700800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr18:44678000-44701000	Weak transcription	Fetal Stomach	stomach
14	chr18:44678200-44690800	Weak transcription	Fetal Intestine Small	intestine
15	chr18:44678200-44692400	Weak transcription	Thymus	Thymus
16	chr18:44678200-44692600	Weak transcription	NHLF	lung
17	chr18:44678200-44700200	Weak transcription	Brain Angular Gyrus	brain
18	chr18:44678200-44700800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr18:44678200-44701000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr18:44678200-44701200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr18:44678200-44701200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr18:44678400-44692200	Weak transcription	Right Ventricle	heart
23	chr18:44678400-44695400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr18:44678400-44700000	Weak transcription	Psoas Muscle	Psoas
25	chr18:44678400-44700800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr18:44678400-44700800	Weak transcription	Lung	lung
27	chr18:44678600-44691200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr18:44678600-44699000	Weak transcription	Dnd41	blood
29	chr18:44681200-44692200	Weak transcription	Ovary	ovary
30	chr18:44681200-44699000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr18:44681200-44699600	Weak transcription	Fetal Muscle Leg	muscle
32	chr18:44681200-44699600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr18:44681200-44699800	Weak transcription	Left Ventricle	heart
34	chr18:44681400-44699600	Weak transcription	Primary T cells from cord blood	blood
35	chr18:44681600-44700200	Weak transcription	Fetal Kidney	kidney
36	chr18:44681800-44690800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr18:44681800-44692800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr18:44681800-44699400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr18:44681800-44699800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr18:44681800-44700200	Weak transcription	HSMM	muscle
41	chr18:44681800-44700800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr18:44681800-44700800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr18:44681800-44700800	Weak transcription	Placenta	Placenta
44	chr18:44681800-44701000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr18:44681800-44701000	Weak transcription	Fetal Thymus	thymus
46	chr18:44681800-44701200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr18:44682000-44691600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr18:44682400-44700200	Weak transcription	Liver	Liver
49	chr18:44682400-44701000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr18:44682600-44698800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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