Variant report

Variant	rs1198422
Chromosome Location	chr13:50155742-50155743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50152416..50157405-chr13:50158007..50161090,7	MCF-7	breast:
2	chr13:50147102..50149993-chr13:50155282..50157133,2	MCF-7	breast:
3	chr13:50153114..50155193-chr13:50155306..50157479,2	MCF-7	breast:
4	chr13:50140695..50143077-chr13:50154599..50156492,2	K562	blood:

Variant related genes	Relation type
ENSG00000136144	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1198421	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359542	0.98[ASN][1000 genomes]
rs1536192	0.90[JPT][hapmap]
rs1570883	0.90[JPT][hapmap]
rs1886793	0.83[ASN][1000 genomes]
rs1998780	0.90[JPT][hapmap]
rs1998781	0.90[JPT][hapmap]
rs2104183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2146145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2209506	0.86[ASN][1000 genomes]
rs2274278	0.90[JPT][hapmap]
rs2274284	0.81[JPT][hapmap]
rs2407697	0.90[JPT][hapmap]
rs3794376	0.90[JPT][hapmap]
rs4572288	0.88[ASN][1000 genomes]
rs4941648	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4941650	0.98[ASN][1000 genomes]
rs5007254	0.88[ASN][1000 genomes]
rs6561539	0.90[JPT][hapmap]
rs6561542	0.90[JPT][hapmap]
rs7139724	0.98[ASN][1000 genomes]
rs7317140	0.90[JPT][hapmap]
rs7324024	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7986405	0.95[ASN][1000 genomes]
rs7992691	0.88[ASN][1000 genomes]
rs7994516	0.81[ASN][1000 genomes]
rs7996012	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs8000962	0.88[ASN][1000 genomes]
rs9526577	0.84[JPT][hapmap]
rs9535259	0.90[JPT][hapmap]
rs9535262	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9535269	0.98[ASN][1000 genomes]
rs9562896	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs9596161	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
13	esv2761789	chr13:50122852-50185910	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv455883	chr13:50124621-50185204	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv561617	chr13:50124621-50185204	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1198422	FGD5	trans	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50108600-50158800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:50122000-50158000	Weak transcription	Brain Germinal Matrix	brain
3	chr13:50124000-50158800	Weak transcription	Esophagus	oesophagus
4	chr13:50129000-50158800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr13:50130400-50158800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:50134200-50158400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr13:50134200-50158400	Weak transcription	Fetal Brain Female	brain
8	chr13:50135000-50158600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr13:50135600-50158000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:50135600-50158400	Weak transcription	Osteobl	bone
11	chr13:50138600-50157200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:50139400-50159000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr13:50140800-50158000	Weak transcription	Fetal Brain Male	brain
14	chr13:50141200-50158000	Weak transcription	NHDF-Ad	bronchial
15	chr13:50141400-50158000	Weak transcription	Fetal Lung	lung
16	chr13:50141400-50158600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr13:50142000-50158000	Weak transcription	NHLF	lung
18	chr13:50142200-50158600	Weak transcription	K562	blood
19	chr13:50144600-50158400	Weak transcription	A549	lung
20	chr13:50144800-50158200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr13:50144800-50158200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr13:50145000-50157600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:50145000-50158600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr13:50145800-50158000	Weak transcription	Hela-S3	cervix
25	chr13:50145800-50158200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr13:50149000-50157800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:50149200-50158600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr13:50151400-50157600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr13:50151600-50157600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr13:50151800-50158000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr13:50151800-50158000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr13:50151800-50158600	Weak transcription	Psoas Muscle	Psoas
33	chr13:50151800-50158600	Weak transcription	Right Ventricle	heart
34	chr13:50152000-50157800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr13:50152000-50158600	Weak transcription	Aorta	Aorta
36	chr13:50152200-50156200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr13:50152400-50156200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:50152400-50156200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr13:50152400-50156200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr13:50152400-50157600	Weak transcription	Fetal Heart	heart
41	chr13:50152600-50155800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:50152600-50156000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr13:50152600-50157000	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr13:50152600-50157400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr13:50152800-50156800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr13:50153000-50155800	Strong transcription	Primary T cells from cord blood	blood
47	chr13:50153000-50156200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr13:50153200-50156000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr13:50153200-50156000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr13:50153200-50157600	Weak transcription	Brain Angular Gyrus	brain

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