Variant report

Variant	rs1376109
Chromosome Location	chr4:121838315-121838316
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	chr4:121832110..121834901-chr4:121836477..121839157,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10006503	0.86[ASN][1000 genomes]
rs10857075	0.83[ASN][1000 genomes]
rs10857076	0.86[ASN][1000 genomes]
rs1450459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1450472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1450473	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs1450475	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs1450479	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1511314	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs1530799	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs180730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs180731	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs184668	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs184669	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1901136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2167207	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2198032	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597548	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2667175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2667176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3106313	0.81[CEU][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3114955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3115312	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3115314	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs343178	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs343180	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs343195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343198	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343200	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343202	0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs343203	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs343205	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs343212	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs4833187	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs4833694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs870252	0.86[CHB][hapmap];0.90[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1376109	IL21	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121798200-121842400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:121812000-121839400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:121812800-121839800	Weak transcription	Psoas Muscle	Psoas
4	chr4:121813400-121839400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:121813400-121841600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:121813600-121839800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:121813800-121842400	Weak transcription	NHEK	skin
8	chr4:121814200-121839800	Weak transcription	Pancreas	Pancrea
9	chr4:121814600-121840000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:121814600-121842600	Weak transcription	Right Ventricle	heart
11	chr4:121815200-121839800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:121818000-121842400	Weak transcription	NH-A	brain
13	chr4:121821000-121839800	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:121821200-121840000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:121821400-121839800	Weak transcription	Fetal Stomach	stomach
16	chr4:121823800-121842400	Weak transcription	HSMM	muscle
17	chr4:121824800-121840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:121825000-121839800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:121825000-121839800	Weak transcription	Osteobl	bone
20	chr4:121825000-121842600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:121825200-121839200	Weak transcription	Fetal Intestine Small	intestine
22	chr4:121825200-121839800	Weak transcription	Aorta	Aorta
23	chr4:121825600-121842400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:121827600-121842400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:121828000-121839800	Weak transcription	NHDF-Ad	bronchial
26	chr4:121829600-121839400	Weak transcription	Fetal Intestine Large	intestine
27	chr4:121830600-121839400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:121833600-121839800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:121834200-121839000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:121835800-121838400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:121836000-121838400	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr4:121836400-121838400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:121836600-121838400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:121836600-121838800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:121836800-121840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:121837000-121842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:121837200-121839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:121837200-121839800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:121837400-121838600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:121837400-121842600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:121837800-121838400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:121837800-121838400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:121837800-121838400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:121837800-121838400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:121837800-121838400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:121837800-121838400	Enhancers	Fetal Kidney	kidney
47	chr4:121837800-121838400	Enhancers	NHLF	lung
48	chr4:121838000-121838400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr4:121838000-121838400	Enhancers	H9 Cell Line	embryonic stem cell
50	chr4:121838000-121838400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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