Variant report

Variant	rs3799849
Chromosome Location	chr6:110036763-110036764
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10457195	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs10457203	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10499053	0.80[CHB][hapmap];0.90[MKK][hapmap]
rs11153188	0.80[EUR][1000 genomes]
rs11153213	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153214	0.85[ASN][1000 genomes]
rs11153215	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11153216	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11752791	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11754340	0.82[EUR][1000 genomes]
rs11755641	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11968978	0.87[MKK][hapmap]
rs12190372	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12191353	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12192268	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12192776	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12193719	0.83[EUR][1000 genomes]
rs12194061	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs12194157	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12197838	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12197950	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12201356	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12201444	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12203993	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12204548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205140	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12205485	0.85[EUR][1000 genomes]
rs12208018	0.82[EUR][1000 genomes]
rs12208933	0.85[CHB][hapmap]
rs12210706	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12214639	0.81[EUR][1000 genomes]
rs12215077	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12528392	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12528781	0.86[EUR][1000 genomes]
rs13198852	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13199109	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13199135	0.83[EUR][1000 genomes]
rs13201430	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs13201951	0.81[EUR][1000 genomes]
rs1321328	0.85[CHB][hapmap]
rs1322124	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1960325	0.83[EUR][1000 genomes]
rs1980591	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[EUR][1000 genomes]
rs2025147	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2025148	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273752	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36131450	0.80[EUR][1000 genomes]
rs3799845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3899233	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4141930	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4490694	0.82[EUR][1000 genomes]
rs4945833	0.82[EUR][1000 genomes]
rs4947016	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6568592	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6911700	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6914498	0.85[CHB][hapmap]
rs71541003	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs729888	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7341297	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7451512	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7767525	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs971434	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3799849	CD164	cis	parietal	SCAN
rs3799849	FIG4	cis	parietal	SCAN
rs3799849	AKD1	cis	parietal	SCAN
rs3799849	SMPD2	cis	parietal	SCAN
rs3799849	FIG4	cis	cerebellum	SCAN
rs3799849	SMPD2	cis	Whole Blood	GTEx
rs3799849	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs3799849	AKD1	cis	cerebellum	SCAN
rs3799849	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
2	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
3	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
5	chr6:110013400-110038600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:110024200-110038800	Weak transcription	Thymus	Thymus
9	chr6:110024200-110056400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:110025000-110057000	Weak transcription	Fetal Thymus	thymus
11	chr6:110027000-110038200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:110027000-110040400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:110027000-110052400	Weak transcription	Liver	Liver
14	chr6:110027000-110056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:110027600-110038600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:110027800-110038200	Weak transcription	Placenta	Placenta
17	chr6:110028000-110036800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:110028000-110038000	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:110028000-110044000	Weak transcription	Brain Angular Gyrus	brain
20	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:110028200-110036800	Weak transcription	Adipose Nuclei	Adipose
22	chr6:110028200-110037600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:110028200-110057200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:110033200-110041000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:110034200-110039400	Strong transcription	Primary T cells from cord blood	blood
27	chr6:110034400-110041600	Weak transcription	Brain Substantia Nigra	brain
28	chr6:110034400-110042200	Weak transcription	NHLF	lung
29	chr6:110034400-110044400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:110034400-110060800	Weak transcription	Fetal Stomach	stomach
31	chr6:110034600-110037600	Weak transcription	Fetal Intestine Large	intestine
32	chr6:110034600-110041600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:110034600-110041800	Weak transcription	NHDF-Ad	bronchial
34	chr6:110034600-110046600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:110034600-110056400	Weak transcription	Fetal Brain Female	brain
36	chr6:110034600-110057000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:110034800-110037600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:110034800-110038600	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:110034800-110038800	Weak transcription	Fetal Intestine Small	intestine
40	chr6:110034800-110040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:110034800-110042000	Weak transcription	Lung	lung
42	chr6:110034800-110042400	Weak transcription	Brain Anterior Caudate	brain
43	chr6:110034800-110059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:110035000-110044000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
47	chr6:110035200-110039400	Weak transcription	Esophagus	oesophagus
48	chr6:110035200-110040400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:110035200-110056200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:110035200-110065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links