Variant report

Variant	rs7800233
Chromosome Location	chr7:104678877-104678878
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:104672216..104674258-chr7:104678705..104680822,2	K562	blood:
2	chr7:104678746..104681155-chr7:104682249..104684880,2	MCF-7	breast:
3	chr7:104672300..104674897-chr7:104678765..104680844,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LHFPL3-4	chr7:104678832-104678972	NONHSAT122602

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1019040	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10224526	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10231782	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10231975	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10241374	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10242713	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10244764	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10245589	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10245676	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10245796	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10249746	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10249965	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10253962	0.83[EUR][1000 genomes]
rs10260346	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10261472	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10261573	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10264273	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10268866	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10269027	0.82[EUR][1000 genomes]
rs10274607	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10276583	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10279486	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10279602	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10280009	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10280752	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10808139	0.92[EUR][1000 genomes]
rs10808140	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10953464	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10953466	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10953467	0.85[EUR][1000 genomes]
rs11971732	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11973516	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11976329	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11981399	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12531424	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12532062	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12532456	0.86[EUR][1000 genomes]
rs12534140	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12540007	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12667625	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12671368	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12705297	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12705299	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13230660	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2011258	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2058711	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2216107	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2237602	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2237604	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2237605	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2237607	0.81[EUR][1000 genomes]
rs2240453	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2240454	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2240455	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2240457	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2285532	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2299297	0.83[ASN][1000 genomes]
rs2299299	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28434158	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28489493	0.86[EUR][1000 genomes]
rs2891761	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3173872	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3213676	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3213741	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34202980	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34558707	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35780942	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3735377	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4730065	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4730067	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4730068	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4730069	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4730071	0.81[EUR][1000 genomes]
rs6466046	0.82[EUR][1000 genomes]
rs67739707	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6944847	0.81[AMR][1000 genomes]
rs6952534	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6972229	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6973052	0.82[ASN][1000 genomes]
rs71562633	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs740297	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs740298	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs740300	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7780887	0.82[EUR][1000 genomes]
rs7785197	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7787558	0.81[ASN][1000 genomes]
rs7805792	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7810119	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7811349	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs875567	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875568	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs916704	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs960437	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9641340	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9641341	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs999895	0.87[AMR][1000 genomes];0.88[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	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases
2	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	nsv608068	chr7:104622402-104757483	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104656600-104681800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr7:104658600-104681200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:104658600-104703800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:104658800-104681800	Weak transcription	Thymus	Thymus
5	chr7:104659800-104681200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:104661800-104696000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:104663200-104679400	Weak transcription	Fetal Brain Female	brain
8	chr7:104664400-104681200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:104665200-104679200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:104665600-104681600	Weak transcription	NH-A	brain
11	chr7:104665600-104682200	Weak transcription	HMEC	breast
12	chr7:104665600-104682200	Weak transcription	HSMMtube	muscle
13	chr7:104666400-104679600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:104666400-104681000	Weak transcription	NHEK	skin
15	chr7:104666400-104681200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:104666400-104681400	Weak transcription	Colonic Mucosa	Colon
17	chr7:104666800-104681600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:104667000-104681000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:104667000-104681200	Weak transcription	HepG2	liver
20	chr7:104667400-104681000	Weak transcription	Hela-S3	cervix
21	chr7:104667800-104679400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:104668200-104679400	Weak transcription	Fetal Lung	lung
23	chr7:104668200-104685000	Weak transcription	HUVEC	blood vessel
24	chr7:104669200-104679400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr7:104669600-104685000	Weak transcription	Esophagus	oesophagus
26	chr7:104670400-104684400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:104670400-104685000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:104671200-104679400	Weak transcription	Fetal Kidney	kidney
29	chr7:104671600-104680800	Weak transcription	Fetal Heart	heart
30	chr7:104671800-104681800	Weak transcription	Pancreas	Pancrea
31	chr7:104671800-104685000	Weak transcription	Aorta	Aorta
32	chr7:104673000-104685000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:104673200-104681200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:104674600-104681200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:104674800-104679200	Weak transcription	Brain Substantia Nigra	brain
36	chr7:104674800-104679400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:104674800-104679400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr7:104674800-104681200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr7:104674800-104681200	Weak transcription	Osteobl	bone
40	chr7:104674800-104685000	Weak transcription	Right Ventricle	heart
41	chr7:104675000-104679200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:104675000-104679200	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr7:104675000-104679400	Weak transcription	Small Intestine	intestine
44	chr7:104675000-104679600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr7:104675000-104680600	Weak transcription	Fetal Thymus	thymus
46	chr7:104675000-104680600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr7:104675000-104681200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:104675000-104681200	Weak transcription	Ovary	ovary
49	chr7:104675000-104681800	Weak transcription	Fetal Intestine Large	intestine
50	chr7:104675000-104682000	Weak transcription	Fetal Muscle Leg	muscle

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