Variant report

Variant	rs2635049
Chromosome Location	chr18:44687303-44687304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:44676287..44678007-chr18:44686109..44688856,2	MCF-7	breast:
2	chr18:44685820..44687618-chr18:44709763..44711914,2	K562	blood:
3	chr18:44675461..44681646-chr18:44682135..44691602,15	MCF-7	breast:

Variant related genes	Relation type
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]
rs11663321	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12960378	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12960444	0.84[EUR][1000 genomes]
rs12963648	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12964465	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13381713	0.83[GIH][hapmap]
rs16954921	0.86[GIH][hapmap]
rs16954999	0.86[GIH][hapmap]
rs17785419	0.85[CEU][hapmap]
rs2251948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277717	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289133	0.80[GIH][hapmap]
rs2461247	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571001	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571009	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2571016	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576030	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576031	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576053	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2576056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576060	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635041	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635042	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2635043	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635045	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635046	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2635047	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2635050	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668761	0.86[GIH][hapmap]
rs2668779	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2684818	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2684820	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684822	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2684825	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684826	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684837	0.87[CEU][hapmap]
rs28693565	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28702976	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2932126	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3816125	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7242978	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7504798	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9304341	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9960264	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes];0.87[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	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
rs2635049	KATNAL2	cis	parietal	SCAN
rs2635049	PIAS2	cis	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44677600-44700200	Weak transcription	Aorta	Aorta
2	chr18:44677800-44689800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr18:44677800-44693400	Weak transcription	Gastric	stomach
4	chr18:44677800-44698200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr18:44677800-44699000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr18:44677800-44700400	Weak transcription	Spleen	Spleen
7	chr18:44677800-44701000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:44677800-44701000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr18:44677800-44701000	Weak transcription	A549	lung
10	chr18:44677800-44701800	Weak transcription	Esophagus	oesophagus
11	chr18:44678000-44689200	Weak transcription	GM12878-XiMat	blood
12	chr18:44678000-44699600	Weak transcription	Colon Smooth Muscle	Colon
13	chr18:44678000-44700400	Weak transcription	Small Intestine	intestine
14	chr18:44678000-44700800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr18:44678000-44701000	Weak transcription	Fetal Stomach	stomach
16	chr18:44678200-44689200	Weak transcription	NHEK	skin
17	chr18:44678200-44689800	Weak transcription	HSMMtube	muscle
18	chr18:44678200-44690800	Weak transcription	Fetal Intestine Small	intestine
19	chr18:44678200-44692400	Weak transcription	Thymus	Thymus
20	chr18:44678200-44692600	Weak transcription	NHLF	lung
21	chr18:44678200-44700200	Weak transcription	Brain Angular Gyrus	brain
22	chr18:44678200-44700800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr18:44678200-44701000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr18:44678200-44701200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr18:44678200-44701200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr18:44678400-44689800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr18:44678400-44690000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr18:44678400-44692200	Weak transcription	Right Ventricle	heart
29	chr18:44678400-44695400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr18:44678400-44700000	Weak transcription	Psoas Muscle	Psoas
31	chr18:44678400-44700800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr18:44678400-44700800	Weak transcription	Lung	lung
33	chr18:44678600-44691200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr18:44678600-44699000	Weak transcription	Dnd41	blood
35	chr18:44681200-44687600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr18:44681200-44689200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr18:44681200-44689600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr18:44681200-44689600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr18:44681200-44689600	Weak transcription	HepG2	liver
40	chr18:44681200-44692200	Weak transcription	Ovary	ovary
41	chr18:44681200-44699000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr18:44681200-44699600	Weak transcription	Fetal Muscle Leg	muscle
43	chr18:44681200-44699600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr18:44681200-44699800	Weak transcription	Left Ventricle	heart
45	chr18:44681400-44699600	Weak transcription	Primary T cells from cord blood	blood
46	chr18:44681600-44700200	Weak transcription	Fetal Kidney	kidney
47	chr18:44681800-44689200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr18:44681800-44689600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr18:44681800-44689600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr18:44681800-44690800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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