Variant report

Variant	rs12194338
Chromosome Location	chr6:143169081-143169082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143166680..143169916-chr6:143203323..143206412,3	MCF-7	breast:
2	chr6:143167641..143169148-chr6:143195736..143197649,2	K562	blood:
3	chr6:143167088..143169502-chr6:143267608..143269824,2	MCF-7	breast:
4	chr6:143168758..143171747-chr6:143172682..143174626,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11155265	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11969269	0.88[ASN][1000 genomes]
rs11969311	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12190804	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12192692	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12194808	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12196693	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12199711	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12201734	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12201987	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12203708	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12205948	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12206012	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12208876	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12210048	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12210301	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12214573	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17444447	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs198661	0.80[EUR][1000 genomes]
rs2142938	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2184364	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2876528	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4349826	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4492208	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62430707	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62430709	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62430712	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62430713	0.88[EUR][1000 genomes]
rs62432360	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62432362	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6905453	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6910072	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6912129	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6925118	0.82[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6927858	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs728589	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72990282	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72995085	0.82[EUR][1000 genomes]
rs972119	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs998313	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv538459	chr6:143165802-143360098	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143165800-143169800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:143166200-143169400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:143167000-143171400	Enhancers	Primary B cells from cord blood	blood
4	chr6:143167200-143169800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:143167200-143172800	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:143167200-143172800	Enhancers	Adipose Nuclei	Adipose
7	chr6:143167200-143177000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:143167400-143169800	Enhancers	Fetal Lung	lung
9	chr6:143167400-143170000	Enhancers	Colon Smooth Muscle	Colon
10	chr6:143167400-143170600	Enhancers	Fetal Kidney	kidney
11	chr6:143167400-143172000	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr6:143167400-143172600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:143167400-143175000	Weak transcription	Right Ventricle	heart
14	chr6:143167600-143169200	Enhancers	Fetal Brain Female	brain
15	chr6:143167600-143169600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr6:143167600-143169800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:143167600-143170800	Weak transcription	Psoas Muscle	Psoas
18	chr6:143167600-143171800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:143167600-143172000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:143167800-143169200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr6:143167800-143170000	Enhancers	Fetal Heart	heart
22	chr6:143167800-143171200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:143167800-143174800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:143167800-143176600	Enhancers	Primary T cells from cord blood	blood
25	chr6:143168000-143169600	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr6:143168000-143171000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:143168200-143169400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr6:143168200-143170000	Weak transcription	Fetal Intestine Large	intestine
29	chr6:143168200-143170000	Weak transcription	Stomach Mucosa	stomach
30	chr6:143168200-143170200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:143168200-143170200	Enhancers	GM12878-XiMat	blood
32	chr6:143168200-143170200	Enhancers	Osteobl	bone
33	chr6:143168200-143170800	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr6:143168200-143170800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:143168200-143171800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:143168200-143176000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:143168400-143169400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr6:143168400-143169400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr6:143168400-143169400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:143168400-143169400	Enhancers	HSMM	muscle
41	chr6:143168400-143169600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:143168400-143169600	Weak transcription	Fetal Thymus	thymus
43	chr6:143168400-143169600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:143168400-143169600	Weak transcription	Thymus	Thymus
45	chr6:143168400-143169800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:143168400-143169800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr6:143168400-143169800	Enhancers	HUVEC	blood vessel
48	chr6:143168400-143170000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:143168400-143170800	Weak transcription	Brain Substantia Nigra	brain
50	chr6:143168400-143170800	Weak transcription	Small Intestine	intestine

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