Variant report

Variant	rs1220397
Chromosome Location	chr1:9993364-9993365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9969076..9970759-chr1:9993245..9994949,2	K562	blood:
2	chr1:9969032..9972214-chr1:9991997..9995260,4	K562	blood:
3	chr1:9992820..9997928-chr1:9999758..10004449,8	K562	blood:
4	chr1:9991529..9996345-chr1:10001160..10004231,6	K562	blood:

Variant related genes	Relation type
ENSG00000173614	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000178585	Chromatin interaction
ENSG00000162441	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11828	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12140009	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12140015	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12140058	0.82[ASN][1000 genomes]
rs1220389	0.85[ASN][1000 genomes]
rs1220398	0.90[CEU][hapmap]
rs1220399	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1220400	0.88[ASN][1000 genomes]
rs1220402	0.83[ASN][1000 genomes]
rs1220420	0.86[ASN][1000 genomes]
rs1220421	0.86[ASN][1000 genomes]
rs1220424	0.83[ASN][1000 genomes]
rs1234694	0.87[ASN][1000 genomes]
rs1628143	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1660733	0.86[ASN][1000 genomes]
rs2890358	0.85[ASN][1000 genomes]
rs2919694	0.83[ASN][1000 genomes]
rs3013783	0.83[ASN][1000 genomes]
rs3013784	0.91[ASN][1000 genomes]
rs6541073	0.85[ASN][1000 genomes]
rs6661806	0.83[ASN][1000 genomes]
rs7517360	0.81[ASN][1000 genomes]
rs7517812	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic 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 lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv534854	chr1:9964726-10001012	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
11	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9971400-9993600	Weak transcription	Aorta	Aorta
2	chr1:9971400-10002000	Weak transcription	Small Intestine	intestine
3	chr1:9972600-10002200	Weak transcription	Right Atrium	heart
4	chr1:9975200-10002600	Weak transcription	Stomach Mucosa	stomach
5	chr1:9983200-10002200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:9983200-10002400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:9983600-10002400	Weak transcription	Fetal Heart	heart
8	chr1:9983600-10002400	Weak transcription	Right Ventricle	heart
9	chr1:9984000-10002200	Weak transcription	HMEC	breast
10	chr1:9984600-9996400	Weak transcription	NHDF-Ad	bronchial
11	chr1:9984600-10002600	Weak transcription	Esophagus	oesophagus
12	chr1:9985200-9996200	Weak transcription	Hela-S3	cervix
13	chr1:9985800-9996200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:9986600-9996800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:9986800-10000200	Strong transcription	Primary T cells from cord blood	blood
16	chr1:9987000-9993600	Weak transcription	Fetal Kidney	kidney
17	chr1:9987000-9996800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:9987000-10002200	Weak transcription	Fetal Brain Male	brain
19	chr1:9987200-9997200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:9987200-10002200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:9987400-10000400	Strong transcription	Fetal Stomach	stomach
22	chr1:9987400-10002000	Weak transcription	Colonic Mucosa	Colon
23	chr1:9987600-9995600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:9987600-9999400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:9987800-9996400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:9987800-9996600	Strong transcription	Adipose Nuclei	Adipose
27	chr1:9987800-9996600	Strong transcription	Liver	Liver
28	chr1:9987800-10002200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:9988000-9996600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr1:9988000-9998600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:9988000-10002000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:9988200-9994800	Weak transcription	Psoas Muscle	Psoas
33	chr1:9988200-9996600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:9988200-10002400	Weak transcription	NHLF	lung
35	chr1:9988400-9994600	Strong transcription	Ovary	ovary
36	chr1:9988400-9996600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:9988400-9996600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:9988400-9996800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:9988400-9997000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:9988400-9997000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:9988400-10000200	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:9988400-10001600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:9988400-10002000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:9988400-10002200	Weak transcription	HUVEC	blood vessel
45	chr1:9988600-9994400	Weak transcription	NH-A	brain
46	chr1:9988600-9996600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:9988600-9996600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:9988600-9996600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:9988600-9996800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:9988600-9996800	Strong transcription	Fetal Thymus	thymus

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