Variant report

Variant	rs12235434
Chromosome Location	chr9:100671500-100671501
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100670192..100672522-chr9:100853837..100856499,2	K562	blood:
2	chr9:100647081..100648971-chr9:100671195..100672929,2	K562	blood:
3	chr9:100667967..100674161-chr9:100680279..100686236,11	K562	blood:
4	chr9:100668512..100673720-chr9:100674176..100679549,8	K562	blood:
5	chr9:100662130..100664191-chr9:100669480..100671871,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HEMGN-3	chr9:100671100-100671593	l_3819_chr9:100671099-100674605_testes

No data

Variant related genes	Relation type
ENSG00000106785	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000201830	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10984193	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10984297	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10984349	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984361	0.97[ASN][1000 genomes]
rs10984375	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10984405	0.83[ASN][1000 genomes]
rs10984462	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10984478	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10984484	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10984499	0.81[ASN][1000 genomes]
rs10984588	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10984599	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1127703	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236440	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377604	0.84[ASN][1000 genomes]
rs1475695	0.89[ASN][1000 genomes]
rs1475696	0.85[ASN][1000 genomes]
rs17346310	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17431614	0.97[ASN][1000 genomes]
rs17431934	0.84[ASN][1000 genomes]
rs3780416	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780417	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780418	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780419	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808894	0.97[ASN][1000 genomes]
rs3824496	0.97[ASN][1000 genomes]
rs4498663	0.82[EUR][1000 genomes]
rs4618817	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4743145	0.97[ASN][1000 genomes]
rs62574034	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62574035	0.85[EUR][1000 genomes]
rs66990486	0.97[ASN][1000 genomes]
rs67500034	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67975003	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68053069	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs68112593	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7024281	0.86[AMR][1000 genomes]
rs7025609	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7030887	0.97[ASN][1000 genomes]
rs7030907	0.97[ASN][1000 genomes]
rs7040232	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72753548	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72753572	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72753587	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs755109	0.84[ASN][1000 genomes]
rs7855917	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7861658	0.97[ASN][1000 genomes]
rs7864655	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100656800-100672400	Weak transcription	Stomach Mucosa	stomach
2	chr9:100658200-100671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:100658400-100671600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr9:100658600-100671600	Weak transcription	Ovary	ovary
5	chr9:100658600-100671600	Weak transcription	Small Intestine	intestine
6	chr9:100658600-100672200	Weak transcription	Esophagus	oesophagus
7	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:100663000-100672200	Weak transcription	Colonic Mucosa	Colon
10	chr9:100663200-100671600	Weak transcription	HSMMtube	muscle
11	chr9:100663200-100671800	Weak transcription	NH-A	brain
12	chr9:100663200-100672000	Weak transcription	HepG2	liver
13	chr9:100663200-100672200	Weak transcription	HSMM	muscle
14	chr9:100663400-100671600	Weak transcription	NHDF-Ad	bronchial
15	chr9:100663400-100672600	Weak transcription	A549	lung
16	chr9:100664000-100673200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:100664400-100672200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:100665400-100671600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:100665400-100679000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:100665600-100671600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:100665600-100678200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:100665800-100671800	Weak transcription	HMEC	breast
23	chr9:100666200-100671600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:100666600-100675400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:100666600-100676000	Strong transcription	Fetal Intestine Large	intestine
26	chr9:100666800-100675800	Strong transcription	Fetal Stomach	stomach
27	chr9:100667000-100675800	Strong transcription	Fetal Intestine Small	intestine
28	chr9:100667200-100679400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:100667200-100684200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:100667400-100671600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr9:100667400-100671600	Weak transcription	NHEK	skin
32	chr9:100667400-100672200	Weak transcription	Fetal Lung	lung
33	chr9:100667600-100671800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr9:100667600-100672000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr9:100667800-100671600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:100667800-100671600	Weak transcription	Osteobl	bone
37	chr9:100667800-100672200	Weak transcription	Psoas Muscle	Psoas
38	chr9:100667800-100674000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:100668000-100671600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:100668000-100672400	Weak transcription	Fetal Kidney	kidney
41	chr9:100668800-100671600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:100669000-100674600	Weak transcription	HUVEC	blood vessel
43	chr9:100669400-100671600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr9:100669400-100671600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:100669400-100672800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:100669400-100673000	Strong transcription	Hela-S3	cervix
47	chr9:100669400-100673800	Strong transcription	Aorta	Aorta
48	chr9:100669400-100675800	Strong transcription	Brain Germinal Matrix	brain
49	chr9:100669400-100675800	Strong transcription	Fetal Muscle Leg	muscle
50	chr9:100669600-100673600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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