Variant report

Variant	rs1421677
Chromosome Location	chr19:38423737-38423738
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:
3	chr19:38405526..38407086-chr19:38423053..38425586,2	MCF-7	breast:
4	chr19:38423561..38425591-chr19:38488215..38490133,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10401880	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10420417	0.80[EUR][1000 genomes]
rs1421676	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305105	0.86[EUR][1000 genomes]
rs2382623	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802150	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4803525	0.86[EUR][1000 genomes]
rs6508753	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs697434	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs705496	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705497	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7257190	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7257688	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8105305	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8108245	0.86[EUR][1000 genomes]
rs833917	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs941038	0.84[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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
5	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:38412000-38423800	Weak transcription	Lung	lung
8	chr19:38418800-38425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:38419400-38424800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:38420200-38425000	Weak transcription	Small Intestine	intestine
11	chr19:38421200-38424400	Enhancers	Fetal Heart	heart
12	chr19:38421200-38425000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:38421600-38424800	Enhancers	Fetal Thymus	thymus
14	chr19:38421800-38423800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr19:38421800-38425400	Enhancers	Fetal Muscle Trunk	muscle
16	chr19:38421800-38425400	Enhancers	Fetal Muscle Leg	muscle
17	chr19:38422000-38426400	Weak transcription	Primary T cells from cord blood	blood
18	chr19:38422200-38425000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:38422200-38425600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:38422400-38423800	Flanking Active TSS	NHEK	skin
21	chr19:38422400-38424000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr19:38422400-38424200	Flanking Active TSS	GM12878-XiMat	blood
23	chr19:38422400-38424400	Active TSS	Rectal Smooth Muscle	rectum
24	chr19:38422400-38424600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38422400-38424800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:38422400-38424800	Enhancers	Left Ventricle	heart
27	chr19:38422400-38424800	Enhancers	HUVEC	blood vessel
28	chr19:38422400-38425000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:38422400-38425000	Enhancers	Psoas Muscle	Psoas
30	chr19:38422400-38425000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr19:38422600-38424400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr19:38422600-38424400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr19:38422600-38425000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:38422800-38424000	Active TSS	Colonic Mucosa	Colon
35	chr19:38422800-38424000	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr19:38423000-38423800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:38423000-38424000	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr19:38423000-38424000	Active TSS	Duodenum Mucosa	Duodenum
39	chr19:38423000-38424200	Active TSS	Fetal Intestine Large	intestine
40	chr19:38423000-38424200	Weak transcription	Fetal Lung	lung
41	chr19:38423000-38424200	Active TSS	Gastric	stomach
42	chr19:38423000-38424200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr19:38423000-38424400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr19:38423000-38425200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:38423000-38425400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:38423000-38438200	Weak transcription	Brain Angular Gyrus	brain
47	chr19:38423200-38423800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:38423200-38423800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:38423200-38424000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:38423200-38424000	Weak transcription	Adipose Nuclei	Adipose

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