Variant report

Variant	rs12137553
Chromosome Location	chr1:173900918-173900919
allele	C/T
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173899124..173901538-chr1:173904329..173906040,2	MCF-7	breast:
2	chr1:173839047..173840684-chr1:173900730..173903519,2	K562	blood:
3	chr1:173829567..173831571-chr1:173900129..173902507,2	K562	blood:
4	chr1:173836510..173838648-chr1:173900344..173902921,2	K562	blood:
5	chr1:173899572..173902216-chr1:173908109..173910346,2	MCF-7	breast:
6	chr1:173833906..173839819-chr1:173898429..173906150,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RC3H1-2	chr1:173900352-173905313	NONHSAT007713

No data

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000208317	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12138407	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138617	0.89[CEU][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12726819	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12746886	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12749768	1.00[ASN][1000 genomes]
rs34997480	1.00[ASN][1000 genomes]
rs35872531	1.00[ASN][1000 genomes]
rs55762016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55842601	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9660185	0.89[CEU][hapmap];1.00[GIH][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
3	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv3407396	chr1:173896346-173917122	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
3	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
4	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
5	chr1:173882800-173912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:173893400-173908400	Weak transcription	Colonic Mucosa	Colon
7	chr1:173894000-173904800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:173894400-173905000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:173894600-173907800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:173894600-173914400	Weak transcription	Right Ventricle	heart
11	chr1:173895000-173902400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:173895000-173903400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:173895200-173912200	Weak transcription	Stomach Mucosa	stomach
14	chr1:173895400-173907600	Weak transcription	Ovary	ovary
15	chr1:173895600-173901200	Weak transcription	HUVEC	blood vessel
16	chr1:173895600-173906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:173895800-173906200	Weak transcription	HepG2	liver
18	chr1:173896400-173901400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:173896400-173902800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:173896400-173907800	Weak transcription	Gastric	stomach
21	chr1:173896400-173910000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:173896400-173914400	Weak transcription	Pancreas	Pancrea
23	chr1:173896600-173902800	Weak transcription	Adipose Nuclei	Adipose
24	chr1:173896800-173908400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:173897000-173907800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:173897000-173908400	Weak transcription	Fetal Intestine Small	intestine
27	chr1:173897400-173907200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:173897600-173903600	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:173897600-173907200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:173897800-173907600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:173898000-173901600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:173898000-173901600	Weak transcription	HSMM	muscle
33	chr1:173898000-173902200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:173898000-173903200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:173898000-173903400	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:173898000-173907800	Weak transcription	Fetal Stomach	stomach
37	chr1:173898000-173915200	Weak transcription	Aorta	Aorta
38	chr1:173898200-173901600	Weak transcription	Placenta	Placenta
39	chr1:173898200-173902400	Weak transcription	Fetal Lung	lung
40	chr1:173898200-173903600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:173898200-173904800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:173898200-173907800	Weak transcription	Thymus	Thymus
43	chr1:173898200-173908800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:173898200-173910000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:173898200-173910200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:173898200-173912200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:173898400-173903600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:173898400-173907200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:173898600-173901400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:173898600-173905400	Weak transcription	Rectal Smooth Muscle	rectum

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