Variant report

Variant	rs996199
Chromosome Location	chr3:98611819-98611820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98605105..98607853-chr3:98609864..98612381,4	K562	blood:
2	chr3:98602528..98604913-chr3:98611525..98613667,2	K562	blood:
3	chr3:98610185..98614055-chr3:98618710..98621878,5	MCF-7	breast:
4	chr3:98609933..98612061-chr3:98623742..98626335,2	K562	blood:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction
ENSG00000239462	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10935512	0.86[AFR][1000 genomes]
rs12330381	0.87[ASN][1000 genomes]
rs13094707	0.87[ASN][1000 genomes]
rs13318536	0.87[ASN][1000 genomes]
rs13318960	0.80[ASN][1000 genomes]
rs13327449	0.80[ASN][1000 genomes]
rs13327485	0.80[ASN][1000 genomes]
rs1351496	0.95[AFR][1000 genomes]
rs1383908	0.98[AFR][1000 genomes]
rs1440157	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs1531736	0.95[AFR][1000 genomes]
rs1600788	0.97[AFR][1000 genomes]
rs1818053	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1972432	0.95[AFR][1000 genomes]
rs2128053	0.98[AFR][1000 genomes]
rs2133575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173598	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs2439230	0.86[AFR][1000 genomes]
rs2439232	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2439234	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2439235	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2448985	0.84[AFR][1000 genomes]
rs2454672	0.94[AFR][1000 genomes]
rs2454681	0.95[AFR][1000 genomes]
rs2454683	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs2454687	1.00[ASN][1000 genomes]
rs2454690	0.85[AFR][1000 genomes]
rs2470820	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs2470828	0.81[AFR][1000 genomes]
rs2470839	0.82[AFR][1000 genomes]
rs2470850	0.80[YRI][hapmap]
rs2470856	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2470858	0.97[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2470866	0.85[AFR][1000 genomes]
rs2470868	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs2470874	0.88[AFR][1000 genomes]
rs2470883	0.98[AFR][1000 genomes]
rs2470884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278375	0.92[YRI][hapmap]
rs278384	1.00[YRI][hapmap]
rs278385	1.00[YRI][hapmap]
rs28528154	0.80[ASN][1000 genomes]
rs28637457	0.87[ASN][1000 genomes]
rs28650813	0.80[ASN][1000 genomes]
rs28821579	0.87[ASN][1000 genomes]
rs28883308	0.80[ASN][1000 genomes]
rs2929491	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs34693680	0.87[ASN][1000 genomes]
rs4273318	0.98[AFR][1000 genomes]
rs4857107	0.92[AFR][1000 genomes]
rs5013928	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6795351	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7373983	0.84[AFR][1000 genomes]
rs7621508	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626395	0.88[AFR][1000 genomes]
rs7630797	0.92[AFR][1000 genomes]
rs828604	0.92[YRI][hapmap]
rs828606	1.00[YRI][hapmap]
rs828607	1.00[YRI][hapmap]
rs828611	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs828622	0.81[AFR][1000 genomes]
rs866873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs9289696	0.87[ASN][1000 genomes]
rs9289700	0.87[ASN][1000 genomes]
rs9819279	0.87[ASN][1000 genomes]
rs9819309	0.87[ASN][1000 genomes]
rs9828045	0.87[ASN][1000 genomes]
rs9842226	0.87[ASN][1000 genomes]
rs9848335	0.87[ASN][1000 genomes]
rs9850469	0.87[ASN][1000 genomes]
rs9852889	0.87[ASN][1000 genomes]
rs9859042	0.87[ASN][1000 genomes]
rs9864010	0.87[ASN][1000 genomes]
rs9872073	0.80[ASN][1000 genomes]
rs9872301	0.80[ASN][1000 genomes]
rs9879302	0.87[ASN][1000 genomes]
rs9883226	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
3	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
5	chr3:98600600-98613000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
8	chr3:98602200-98613600	Genic enhancers	HSMM	muscle
9	chr3:98602400-98613600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:98603200-98612600	Genic enhancers	NHEK	skin
11	chr3:98604000-98613000	Enhancers	NHLF	lung
12	chr3:98604200-98612600	Enhancers	NHDF-Ad	bronchial
13	chr3:98604400-98614600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:98604800-98612600	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
16	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
17	chr3:98606600-98612600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:98606600-98618000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:98607800-98612000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:98608000-98612400	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:98608800-98612000	Enhancers	Ovary	ovary
22	chr3:98608800-98614400	Enhancers	K562	blood
23	chr3:98609000-98612000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:98609000-98612000	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:98609000-98612600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:98609000-98612800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:98609000-98613200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:98609000-98615800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr3:98609200-98613400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:98609400-98612000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:98609400-98613400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr3:98609400-98613800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:98609600-98613400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:98609800-98612000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:98609800-98613800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:98609800-98614200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:98610000-98612800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:98610200-98612600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:98610400-98612000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:98610400-98612000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:98610400-98612000	Enhancers	Psoas Muscle	Psoas
42	chr3:98610400-98615000	Transcr. at gene 5' and 3'	Osteobl	bone
43	chr3:98610400-98615800	Transcr. at gene 5' and 3'	NH-A	brain
44	chr3:98610400-98616600	Transcr. at gene 5' and 3'	A549	lung
45	chr3:98610600-98613400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr3:98610800-98612600	Weak transcription	HSMMtube	muscle
47	chr3:98610800-98614200	Enhancers	Right Ventricle	heart
48	chr3:98610800-98618400	Weak transcription	Brain Anterior Caudate	brain
49	chr3:98610800-98618400	Enhancers	Fetal Heart	heart
50	chr3:98610800-98618600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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