Variant report

Variant	rs9861992
Chromosome Location	chr3:121432535-121432536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12489511	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12490565	0.95[CEU][hapmap];0.92[CHB][hapmap]
rs12631824	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13067629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1492177	0.95[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs1574655	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1574735	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17849995	0.80[EUR][1000 genomes]
rs1873645	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap];0.92[EUR][1000 genomes]
rs1919552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1919557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1986351	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1986874	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2001390	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070179	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2332056	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs2840143	0.95[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes]
rs35295338	0.85[EUR][1000 genomes]
rs3772127	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4478028	0.80[EUR][1000 genomes]
rs4676684	0.90[EUR][1000 genomes]
rs4676685	0.92[EUR][1000 genomes]
rs4676686	0.91[EUR][1000 genomes]
rs4676690	0.84[ASN][1000 genomes]
rs4676751	0.81[EUR][1000 genomes]
rs59740137	0.80[EUR][1000 genomes]
rs6438645	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6438660	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs6770719	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs6776703	0.81[EUR][1000 genomes]
rs6791896	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792659	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6794341	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794677	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6802033	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6803839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6807711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73179983	0.84[ASN][1000 genomes]
rs7375038	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes]
rs7429247	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7430165	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7611913	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7620842	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7646346	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs7646585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289172	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9289173	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9681209	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs9809114	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9812411	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9829053	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9832267	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835182	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9854052	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864907	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9876021	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised 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	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9861992	HCLS1	cis	multi-tissue	Pritchard
rs9861992	HCLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:121396800-121435600	Weak transcription	Psoas Muscle	Psoas
3	chr3:121399000-121440400	Weak transcription	K562	blood
4	chr3:121401200-121434000	Weak transcription	Gastric	stomach
5	chr3:121404000-121432800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:121410400-121435600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:121411000-121432800	Weak transcription	Fetal Brain Male	brain
8	chr3:121411000-121442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:121411400-121432800	Weak transcription	Colonic Mucosa	Colon
10	chr3:121411400-121437200	Weak transcription	Small Intestine	intestine
11	chr3:121413400-121446200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:121414800-121436200	Weak transcription	Stomach Mucosa	stomach
13	chr3:121417200-121435800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:121417600-121432800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:121417600-121432800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:121417600-121434200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:121417600-121434200	Weak transcription	Aorta	Aorta
18	chr3:121417600-121435200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:121417600-121437200	Weak transcription	Spleen	Spleen
20	chr3:121418000-121434200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:121418000-121435400	Weak transcription	NHLF	lung
22	chr3:121418800-121442000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:121419600-121436200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:121419800-121434400	Weak transcription	HUVEC	blood vessel
25	chr3:121420200-121432600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:121420200-121433000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:121421000-121432600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:121421200-121435200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:121421400-121436600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:121421400-121436600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:121421600-121433000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:121421600-121434200	Weak transcription	Left Ventricle	heart
33	chr3:121424600-121435400	Weak transcription	Right Ventricle	heart
34	chr3:121424800-121432800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:121426200-121442600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:121426200-121443200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:121426400-121434000	Weak transcription	Lung	lung
38	chr3:121426600-121432600	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:121426600-121433600	Weak transcription	Ovary	ovary
40	chr3:121426600-121434000	Weak transcription	Thymus	Thymus
41	chr3:121426600-121434200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:121427000-121436600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:121427400-121433600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:121427400-121435400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:121428600-121438200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:121428800-121436400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:121429000-121450000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:121429400-121442800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:121429400-121448800	Strong transcription	Primary hematopoietic stem cells	blood
50	chr3:121429400-121449000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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