Variant report

Variant	rs3213741
Chromosome Location	chr7:104643111-104643112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRPK2-1	chr7:104637584-104654636	NONHSAT122594

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1013016	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1019040	0.83[EUR][1000 genomes]
rs10224526	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10231782	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10231975	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241374	0.83[EUR][1000 genomes]
rs10242713	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10244764	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10245589	0.89[EUR][1000 genomes]
rs10245676	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10245796	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10249746	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10249965	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10253962	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10260346	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10261472	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10261573	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10264273	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10268866	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10274607	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10276583	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10279486	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10279602	0.88[EUR][1000 genomes]
rs10280009	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10280752	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10808139	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10808140	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10953464	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10953466	0.82[EUR][1000 genomes]
rs10953467	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11971732	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11973516	0.82[AMR][1000 genomes]
rs11976329	0.88[EUR][1000 genomes]
rs11981399	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12171585	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12531424	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12532062	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12532456	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12534140	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12540007	0.88[EUR][1000 genomes]
rs12667625	0.83[EUR][1000 genomes]
rs12671368	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12705297	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12705299	0.86[EUR][1000 genomes]
rs13230660	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967301	0.80[AMR][1000 genomes]
rs2011258	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2058711	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216107	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237602	0.88[EUR][1000 genomes]
rs2237604	0.84[EUR][1000 genomes]
rs2237605	0.88[EUR][1000 genomes]
rs2240453	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2240454	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2240455	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2240457	0.88[EUR][1000 genomes]
rs2285532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299299	0.86[EUR][1000 genomes]
rs28434158	0.83[EUR][1000 genomes]
rs28489493	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2891761	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3173872	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3213676	0.88[EUR][1000 genomes]
rs34202980	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34558707	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35418021	0.80[AMR][1000 genomes]
rs35780942	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3735377	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3815256	0.82[AMR][1000 genomes]
rs4730065	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4730067	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4730068	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4730069	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6466043	0.85[AMR][1000 genomes]
rs6466045	0.82[AMR][1000 genomes]
rs67739707	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6952534	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6972229	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71562633	0.86[EUR][1000 genomes]
rs740297	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs740298	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs740300	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7785197	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7800233	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7805792	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7810119	0.88[EUR][1000 genomes]
rs7811349	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs875567	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs875568	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs916704	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960437	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9641340	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9641341	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs999895	0.83[AMR][1000 genomes];0.89[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	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	esv2829879	chr7:104618318-104652671	Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	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
5	nsv437561	chr7:104626690-104647571	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022083	chr7:104634376-104644391	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104625000-104647400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:104625200-104643800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:104627400-104643600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:104630800-104643600	Weak transcription	Fetal Kidney	kidney
5	chr7:104631600-104643600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:104633200-104643600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr7:104633600-104650400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr7:104634000-104647200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:104635400-104643200	Weak transcription	HUVEC	blood vessel
10	chr7:104635600-104645600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr7:104635800-104643400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:104636400-104645400	Enhancers	Fetal Heart	heart
13	chr7:104636400-104649400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:104637000-104643400	Weak transcription	HepG2	liver
15	chr7:104637200-104643400	Weak transcription	Fetal Lung	lung
16	chr7:104638200-104646800	Enhancers	Stomach Mucosa	stomach
17	chr7:104638400-104643800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:104638400-104645800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:104638600-104643800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr7:104639400-104643400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:104639400-104643600	Enhancers	Adipose Nuclei	Adipose
22	chr7:104639400-104649800	Genic enhancers	Fetal Intestine Small	intestine
23	chr7:104639800-104648800	Enhancers	Colon Smooth Muscle	Colon
24	chr7:104640000-104643400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr7:104640000-104643800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:104640000-104646200	Enhancers	Liver	Liver
27	chr7:104640200-104645600	Enhancers	Brain Angular Gyrus	brain
28	chr7:104640200-104648600	Genic enhancers	Dnd41	blood
29	chr7:104640400-104643800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr7:104640600-104643600	Strong transcription	K562	blood
31	chr7:104640800-104643600	Enhancers	Brain Anterior Caudate	brain
32	chr7:104640800-104645800	Enhancers	Brain Hippocampus Middle	brain
33	chr7:104641000-104643600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr7:104641400-104643200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr7:104641400-104643400	Genic enhancers	Rectal Mucosa Donor 31	rectum
36	chr7:104641400-104643600	Enhancers	Duodenum Mucosa	Duodenum
37	chr7:104641600-104643600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr7:104641800-104643400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr7:104641800-104643400	Weak transcription	Aorta	Aorta
40	chr7:104641800-104643400	Weak transcription	HMEC	breast
41	chr7:104641800-104643600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:104641800-104643600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:104641800-104643600	Weak transcription	Fetal Muscle Leg	muscle
44	chr7:104641800-104643600	Weak transcription	Gastric	stomach
45	chr7:104641800-104643600	Weak transcription	Spleen	Spleen
46	chr7:104641800-104643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr7:104641800-104643800	Weak transcription	Right Ventricle	heart
48	chr7:104641800-104643800	Weak transcription	Thymus	Thymus
49	chr7:104641800-104646000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:104641800-104646000	Weak transcription	Lung	lung

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