Variant report

Variant	rs12197001
Chromosome Location	chr6:38143476-38143477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38140845..38143617-chr6:38230207..38231726,2	MCF-7	breast:
2	chr6:38143259..38145952-chr6:38146356..38150615,4	K562	blood:
3	chr6:38143298..38146088-chr6:38153690..38155707,2	K562	blood:
4	chr6:38137479..38141029-chr6:38143334..38147856,5	K562	blood:
5	chr6:38138220..38140617-chr6:38142892..38144834,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZFAND3-4	chr6:38142931-38144082	NONHSAT112308

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10807190	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10807191	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10807192	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10947714	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10947716	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11754110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11756830	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196879	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12198616	0.92[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs12206712	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13205068	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13212638	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs17678747	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs17678833	0.87[ASN][1000 genomes]
rs2143403	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235710	0.94[ASN][1000 genomes]
rs2235711	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3800358	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs3823431	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4314486	0.94[ASN][1000 genomes]
rs4510661	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs6458044	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6938410	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs735117	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs737171	0.93[ASN][1000 genomes]
rs742537	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs742538	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs742539	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs761153	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7742915	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7756835	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs909998	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs926565	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9380721	0.94[ASN][1000 genomes]
rs9462400	0.93[ASN][1000 genomes]
rs9462404	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9462405	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9462406	0.83[ASN][1000 genomes]
rs9462409	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9470806	0.82[ASN][1000 genomes]
rs9470807	0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9470811	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9470813	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9470816	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470818	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470819	0.93[ASN][1000 genomes]
rs9470820	0.93[ASN][1000 genomes]
rs9470822	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470823	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470824	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470825	0.81[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv524213	chr6:38106844-38160627	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv517973	chr6:38131442-38152460	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
9	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38121000-38159600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38121800-38153600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr6:38123200-38153200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:38123400-38155400	Weak transcription	Aorta	Aorta
5	chr6:38123400-38157000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:38123400-38176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:38123600-38144200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr6:38123600-38153000	Weak transcription	Primary B cells from cord blood	blood
9	chr6:38123800-38151200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:38124000-38152200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:38124200-38151800	Weak transcription	Brain Anterior Caudate	brain
12	chr6:38124400-38144200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:38129200-38145600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:38129400-38144600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:38130000-38144400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:38131200-38143800	Weak transcription	Thymus	Thymus
17	chr6:38131800-38167800	Weak transcription	Right Atrium	heart
18	chr6:38133600-38144600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:38133600-38160400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:38133600-38164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:38136000-38159800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:38136800-38145200	Genic enhancers	Fetal Intestine Small	intestine
23	chr6:38136800-38156000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:38137600-38144200	Strong transcription	Spleen	Spleen
25	chr6:38138200-38143600	Weak transcription	Esophagus	oesophagus
26	chr6:38138200-38147200	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:38138400-38143800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:38138400-38144400	Weak transcription	Pancreas	Pancrea
29	chr6:38138400-38145200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:38138400-38145400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:38138400-38147200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:38138400-38147200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:38138600-38145400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:38138600-38169400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:38138800-38144200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:38138800-38144600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:38138800-38145400	Weak transcription	Fetal Brain Female	brain
38	chr6:38138800-38147200	Weak transcription	Brain Germinal Matrix	brain
39	chr6:38138800-38147200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:38139000-38144600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:38139200-38144200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:38139200-38144800	Weak transcription	HSMM	muscle
43	chr6:38139800-38144400	Strong transcription	Fetal Stomach	stomach
44	chr6:38139800-38145000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:38140000-38143600	Weak transcription	GM12878-XiMat	blood
46	chr6:38140000-38144800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:38140000-38147200	Weak transcription	Brain Angular Gyrus	brain
48	chr6:38140200-38144000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:38140400-38146200	Weak transcription	Small Intestine	intestine
50	chr6:38140800-38144000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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