Variant report

Variant	rs10176989
Chromosome Location	chr2:48982868-48982869
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr2:48981913-48983093	H1-hESC	embryonic stem cell:	n/a	n/a
2	ESR1	chr2:48982776-48983166	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr2:48982766-48983101	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr2:48982566-48983035	ECC-1	luminal epithelium:	n/a	n/a
5	RAD21	chr2:48982526-48983031	H1-hESC	embryonic stem cell:	n/a	n/a
6	ESR1	chr2:48982852-48983133	ECC-1	luminal epithelium:	n/a	n/a
7	E2F6	chr2:48982336-48983038	H1-hESC	embryonic stem cell:	n/a	chr2:48982559-48982570
8	MAX	chr2:48982403-48983017	H1-hESC	embryonic stem cell:	n/a	chr2:48982404-48982414
9	ZNF143	chr2:48982681-48982915	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr2:48982625-48983089	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr2:48982527-48982978	H1-hESC	embryonic stem cell:	n/a	chr2:48982559-48982570
12	YY1	chr2:48982556-48982974	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr2:48982399-48983065	H1-hESC	embryonic stem cell:	n/a	chr2:48982404-48982414
14	TBP	chr2:48982597-48982916	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:48982832-48982882	SK-N-SH	brain:	n/a
2	chr2:48982832-48982882	AG04450	lung:	fetal
3	chr2:48982832-48982882	CMK	blood:	n/a
4	chr2:48982832-48982882	HCF	heart:	n/a
5	chr2:48982832-48982882	BJ	skin:	n/a
6	chr2:48982832-48982882	GM12878	blood:	n/a
7	chr2:48982832-48982882	GM06990	blood:	n/a
8	chr2:48982832-48982882	HPAEpiC	pulmonary alveolar:	n/a
9	chr2:48982832-48982882	NHBE	bronchial:	n/a
10	chr2:48982832-48982882	K562	blood:	n/a
11	chr2:48982832-48982882	AG04449	skin:	fetal
12	chr2:48982832-48982882	GM12891	blood:	n/a
13	chr2:48982832-48982882	NHDF-neo	bronchial:	n/a
14	chr2:48982832-48982882	U87	brain:	n/a
15	chr2:48982832-48982882	HCPEpiC	choroid plexus:	n/a
16	chr2:48982832-48982882	HEEpiC	esophagus:	n/a
17	chr2:48982832-48982882	AG10803	skin:	n/a
18	chr2:48982832-48982882	NH-A	brain:	n/a
19	chr2:48982832-48982882	AG09319	gingival:	n/a
20	chr2:48982832-48982882	LNCaP	prostate:	n/a
21	chr2:48982832-48982882	HL-60	blood:	n/a
22	chr2:48982832-48982882	Hepatocyte	liver:	n/a
23	chr2:48982832-48982882	Caco-2	colon:	n/a
24	chr2:48982832-48982882	HRCEpiC	kidney:	n/a
25	chr2:48982832-48982882	NT2-D1	testis:	n/a
26	chr2:48982832-48982882	GM12892	blood:	n/a
27	chr2:48982832-48982882	SK-N-MC	brain:	n/a
28	chr2:48982832-48982882	AoSMC	blood vessel:	n/a
29	chr2:48982832-48982882	SK-N-SH_RA	brain:	n/a
30	chr2:48982832-48982882	HepG2	liver:	n/a
31	chr2:48982832-48982882	RPTEC	kidney:	n/a
32	chr2:48982832-48982882	ovcar-3	ovarian:	n/a
33	chr2:48982832-48982882	PFSK-1	brain:	n/a
34	chr2:48982832-48982882	Hela-S3	cervix:	n/a
35	chr2:48982832-48982882	SKMC	muscle:	n/a
36	chr2:48982832-48982882	HCT-116	colon:	n/a
37	chr2:48982832-48982882	HMEC	breast:	n/a
38	chr2:48982832-48982882	ProgFib	skin:	n/a
39	chr2:48982832-48982882	MCF-7	breast:	n/a
40	chr2:48982832-48982882	BE2_C	brain:	n/a
41	chr2:48982832-48982882	SAEC	small airway:	n/a
42	chr2:48982832-48982882	NB4	blood:	n/a
43	chr2:48982832-48982882	IMR90	lung:	fetal
44	chr2:48982832-48982882	AG09309	skin:	n/a
45	chr2:48982832-48982882	T-47D	breast:	n/a
46	chr2:48982832-48982882	HNPCEpiC	eye:	n/a
47	chr2:48982832-48982882	HUVEC	blood vessel:	n/a
48	chr2:48982832-48982882	PrEC	prostate:	n/a
49	chr2:48982832-48982882	HAEpiC	amniotic membrane:	n/a
50	chr2:48982832-48982882	HRPEpiC	eye:	n/a

No data

Variant related genes	Relation type
LHCGR	TF binding region
LHCGR	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10209331	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10495959	0.85[AMR][1000 genomes]
rs13405728	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13432488	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4075876	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6732721	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6751138	0.85[AMR][1000 genomes]
rs7562879	0.97[ASN][1000 genomes]
rs7563126	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7567846	0.91[ASN][1000 genomes]
rs7582603	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7594589	0.86[AMR][1000 genomes]
rs7595136	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7606567	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS 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	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48981800-48983000	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr2:48982000-48983000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:48982000-48983000	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr2:48982000-48983200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
5	chr2:48982200-48983000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:48982200-48983000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr2:48982200-48983000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr2:48982400-48983000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:48982400-48983000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:48982400-48983000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:48982400-48983000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:48982400-48983000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:48982400-48983000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
14	chr2:48982400-48983000	Bivalent Enhancer	Fetal Intestine Small	intestine
15	chr2:48982400-48983000	Active TSS	Ovary	ovary
16	chr2:48982400-48983200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr2:48982600-48983000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr2:48982600-48983000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:48982600-48983000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
20	chr2:48982600-48983000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:48982600-48983000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:48982600-48983000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
23	chr2:48982600-48983000	Bivalent Enhancer	Fetal Brain Male	brain
24	chr2:48982600-48983000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr2:48982600-48983000	Bivalent/Poised TSS	Osteobl	bone
26	chr2:48982600-48983200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr2:48982800-48983000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr2:48982800-48983000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:48982800-48983000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:48982800-48983000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:48982800-48983000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:48982800-48983000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:48982800-48983000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
34	chr2:48982800-48983000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:48982800-48983000	Active TSS	Brain Cingulate Gyrus	brain
36	chr2:48982800-48983000	Active TSS	Brain Germinal Matrix	brain
37	chr2:48982800-48983000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
38	chr2:48982800-48983000	Bivalent Enhancer	Left Ventricle	heart
39	chr2:48982800-48983000	Flanking Active TSS	Right Atrium	heart
40	chr2:48982800-48983000	Active TSS	Right Ventricle	heart
41	chr2:48982800-48983000	Active TSS	Stomach Smooth Muscle	stomach
42	chr2:48982800-48983200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
43	chr2:48982800-48983200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr2:48982800-48983800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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