Variant report

Variant	rs6721297
Chromosome Location	chr2:99997981-99997982
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99990124..99992990-chr2:99997143..100000018,2	MCF-7	breast:
2	chr2:99996957..100000036-chr2:100003935..100006623,3	K562	blood:

Variant related genes	Relation type
ENSG00000158417	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1000409	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs1011633	0.81[CHB][hapmap]
rs10172068	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[YRI][hapmap]
rs10172752	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[YRI][hapmap]
rs10187843	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs11123775	0.82[CHB][hapmap]
rs11123782	0.95[CHB][hapmap];0.96[YRI][hapmap]
rs11123786	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11676581	0.95[CHB][hapmap];0.95[YRI][hapmap]
rs11683651	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs11686535	1.00[CHB][hapmap];0.96[YRI][hapmap]
rs11687870	0.89[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap]
rs11887574	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs11899745	0.81[CHB][hapmap]
rs11902994	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs12623540	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs13014360	0.95[CHB][hapmap];0.95[YRI][hapmap]
rs13017871	0.82[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap]
rs13018274	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap]
rs13026997	0.95[CHB][hapmap];0.96[YRI][hapmap]
rs1451243	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap]
rs17022433	0.81[CHB][hapmap]
rs2242037	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs2290256	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs2305354	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap]
rs2309585	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[YRI][hapmap]
rs3087386	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[YRI][hapmap]
rs3792134	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[YRI][hapmap]
rs3792137	0.81[CHB][hapmap]
rs3792142	0.81[CHB][hapmap]
rs3792146	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[YRI][hapmap]
rs3792149	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[YRI][hapmap]
rs3792152	1.00[CHB][hapmap];0.92[YRI][hapmap]
rs3811555	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs3828316	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap]
rs4143760	0.82[CHB][hapmap]
rs4535093	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap]
rs4850901	0.82[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap]
rs4851200	0.95[CHB][hapmap];0.83[YRI][hapmap]
rs4851205	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap]
rs4851206	0.81[CHB][hapmap]
rs6542879	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[YRI][hapmap]
rs6542880	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[YRI][hapmap]
rs6542882	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[YRI][hapmap]
rs6708861	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs6711977	0.95[CHB][hapmap];0.95[YRI][hapmap]
rs6714244	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[YRI][hapmap]
rs6722617	0.81[CHB][hapmap]
rs6734290	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs7561079	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs7561616	0.95[CHB][hapmap];0.84[YRI][hapmap]
rs7563462	0.81[CHB][hapmap]
rs7567674	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap]
rs7571202	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs7574135	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs7579403	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap]
rs7580448	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[YRI][hapmap]
rs7585019	0.81[CHB][hapmap]
rs7585721	0.85[CEU][hapmap];0.95[CHB][hapmap];0.96[YRI][hapmap]
rs7587419	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs7594838	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[YRI][hapmap]
rs7601470	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs7601730	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap]
rs769105	0.81[CHB][hapmap]
rs896249	0.82[CHB][hapmap]
rs959929	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[YRI][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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6721297	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6721297	REV1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
2	chr2:99975400-100006400	Weak transcription	Stomach Mucosa	stomach
3	chr2:99976200-100003800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:99976200-100004400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:99976400-100003200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:99976600-100002400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr2:99976600-100004800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:99977000-100001000	Strong transcription	Primary B cells from cord blood	blood
9	chr2:99977000-100001400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:99977000-100003200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:99977000-100003200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:99977000-100003600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:99977000-100003800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:99977000-100003800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:99977600-100002200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:99977600-100003600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:99978200-100011800	Weak transcription	Esophagus	oesophagus
18	chr2:99979400-99999800	Strong transcription	Osteobl	bone
19	chr2:99979400-100001600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr2:99979400-100003600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:99979400-100004200	Strong transcription	Fetal Thymus	thymus
22	chr2:99979600-100002800	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:99979600-100003200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:99979600-100009600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:99979800-100002200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:99979800-100002800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:99982800-100000400	Strong transcription	HSMM	muscle
28	chr2:99983200-100013600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr2:99985600-100006800	Weak transcription	Colonic Mucosa	Colon
30	chr2:99985800-99998800	Weak transcription	Psoas Muscle	Psoas
31	chr2:99987400-99999400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:99988000-100003200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr2:99988200-100001400	Strong transcription	K562	blood
34	chr2:99988400-100001400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:99988400-100001400	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr2:99989000-100003200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:99990000-100006600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:99990000-100012200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:99990200-100010800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:99990600-100006600	Weak transcription	Pancreas	Pancrea
41	chr2:99990600-100010800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:99990600-100010800	Weak transcription	Spleen	Spleen
43	chr2:99990800-99999800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:99990800-100004600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr2:99990800-100007000	Weak transcription	Gastric	stomach
46	chr2:99991200-100003600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:99991400-100001200	Strong transcription	NH-A	brain
48	chr2:99991400-100002400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:99991400-100002400	Strong transcription	Primary T cells from cord blood	blood
50	chr2:99991400-100003200	Strong transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links