Variant report

Variant	rs7646221
Chromosome Location	chr3:99640320-99640321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:99611356..99613226-chr3:99640035..99641945,2	K562	blood:
2	chr3:99638831..99640406-chr3:99649690..99652497,2	K562	blood:
3	chr3:99595540..99598482-chr3:99638199..99641058,2	MCF-7	breast:
4	chr3:99592487..99595071-chr3:99639782..99642342,2	MCF-7	breast:
5	chr3:99639074..99641020-chr3:99643167..99645539,2	K562	blood:
6	chr3:99639208..99643794-chr3:99646040..99649673,4	MCF-7	breast:
7	chr3:99638906..99644679-chr3:99646570..99651799,7	K562	blood:
8	chr3:99589828..99592269-chr3:99639312..99642221,3	K562	blood:
9	chr3:99639154..99641723-chr3:99643232..99645940,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs15890	1.00[AMR][1000 genomes]
rs17313676	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314245	1.00[EUR][1000 genomes]
rs17314280	1.00[EUR][1000 genomes]
rs17314977	1.00[EUR][1000 genomes]
rs17338576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17392822	1.00[EUR][1000 genomes]
rs17393080	1.00[EUR][1000 genomes]
rs17397949	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778707	1.00[AMR][1000 genomes]
rs17778804	1.00[AMR][1000 genomes]
rs17779605	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2035400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762809	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762871	1.00[EUR][1000 genomes]
rs6781780	1.00[EUR][1000 genomes]
rs6784150	1.00[EUR][1000 genomes]
rs6788807	1.00[EUR][1000 genomes]
rs6790187	1.00[EUR][1000 genomes]
rs6794130	1.00[EUR][1000 genomes]
rs6794365	1.00[EUR][1000 genomes]
rs6803576	1.00[AMR][1000 genomes]
rs6805703	0.89[AFR][1000 genomes]
rs6807137	1.00[EUR][1000 genomes]
rs6807615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808420	0.89[AFR][1000 genomes]
rs7611313	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612083	0.89[AFR][1000 genomes]
rs7612089	0.89[AFR][1000 genomes]
rs7619738	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625813	0.89[AFR][1000 genomes]
rs7626214	0.89[AFR][1000 genomes]
rs7626310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7628458	1.00[EUR][1000 genomes]
rs7648943	1.00[EUR][1000 genomes]
rs766777	1.00[EUR][1000 genomes]
rs9756455	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99619600-99644400	Weak transcription	Right Ventricle	heart
3	chr3:99630600-99644600	Weak transcription	NH-A	brain
4	chr3:99634400-99647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:99637200-99641800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:99637600-99641000	Enhancers	Adipose Nuclei	Adipose
7	chr3:99637600-99641600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:99638000-99640600	Enhancers	Fetal Intestine Small	intestine
9	chr3:99638200-99641000	Enhancers	Stomach Mucosa	stomach
10	chr3:99638200-99641800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:99638400-99640400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:99638400-99640400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:99638400-99640400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:99638400-99640400	Enhancers	GM12878-XiMat	blood
15	chr3:99638400-99640800	Enhancers	NHEK	skin
16	chr3:99638400-99641000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:99638400-99641200	Enhancers	HMEC	breast
18	chr3:99638400-99641400	Enhancers	Fetal Intestine Large	intestine
19	chr3:99638600-99640400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:99638600-99640400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:99638600-99640400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr3:99638600-99640400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:99638600-99640400	Enhancers	Esophagus	oesophagus
24	chr3:99638600-99640400	Enhancers	Fetal Muscle Leg	muscle
25	chr3:99638600-99640400	Enhancers	Right Atrium	heart
26	chr3:99638600-99640400	Enhancers	Small Intestine	intestine
27	chr3:99638600-99640600	Enhancers	K562	blood
28	chr3:99638600-99641000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:99638600-99641000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:99638600-99641000	Enhancers	Psoas Muscle	Psoas
31	chr3:99638600-99641000	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr3:99638600-99641200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:99638800-99640400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:99638800-99640400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:99638800-99640400	Enhancers	Liver	Liver
36	chr3:99638800-99640400	Enhancers	Brain Hippocampus Middle	brain
37	chr3:99638800-99640400	Enhancers	Fetal Lung	lung
38	chr3:99638800-99644200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:99639000-99640400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:99639000-99640400	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr3:99639200-99640400	Enhancers	Left Ventricle	heart
42	chr3:99639200-99640400	Enhancers	Pancreas	Pancrea
43	chr3:99639200-99640400	Enhancers	A549	lung
44	chr3:99639200-99640400	Flanking Active TSS	HepG2	liver
45	chr3:99639200-99640400	Enhancers	NHLF	lung
46	chr3:99639200-99641000	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:99639200-99641000	Enhancers	Brain Substantia Nigra	brain
48	chr3:99639200-99641000	Enhancers	Ovary	ovary
49	chr3:99639200-99641400	Enhancers	Osteobl	bone
50	chr3:99639400-99640400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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