Variant report

Variant	rs6466035
Chromosome Location	chr7:104646899-104646900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:104646792..104648750-chr7:104757505..104760148,2	K562	blood:
2	chr17:59485726..59487410-chr7:104646089..104648934,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRPK2-1	chr7:104637584-104654636	NONHSAT122594

Variant related genes	Relation type
ENSG00000121068	Chromatin interaction
ENSG00000135250	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1010340	0.81[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs1011468	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10228174	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10247691	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10252714	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10263499	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11978288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12534212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1558048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs17640472	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17640508	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs2074753	0.84[CEU][hapmap];0.86[YRI][hapmap]
rs2097942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs2106500	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299298	0.88[EUR][1000 genomes]
rs2299305	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2299309	0.84[CEU][hapmap]
rs4602821	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4727618	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730066	0.90[CHD][hapmap];0.93[ASN][1000 genomes]
rs56016333	0.86[ASN][1000 genomes]
rs67665940	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6947388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949073	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs6950894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs6972563	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs6974874	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs6976394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs7796945	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs888086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9918494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases
2	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	esv2829879	chr7:104618318-104652671	Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv608068	chr7:104622402-104757483	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv437561	chr7:104626690-104647571	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104625000-104647400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:104633600-104650400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr7:104634000-104647200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:104636400-104649400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:104639400-104649800	Genic enhancers	Fetal Intestine Small	intestine
6	chr7:104639800-104648800	Enhancers	Colon Smooth Muscle	Colon
7	chr7:104640200-104648600	Genic enhancers	Dnd41	blood
8	chr7:104641800-104649000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr7:104641800-104651800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:104642000-104650200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:104642000-104650600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:104642200-104650000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:104642400-104651000	Weak transcription	Esophagus	oesophagus
14	chr7:104642400-104652200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:104643400-104648200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr7:104643600-104647200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:104643600-104650800	Genic enhancers	Primary B cells from peripheral blood	blood
18	chr7:104644000-104649400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr7:104644200-104647000	Strong transcription	Fetal Thymus	thymus
20	chr7:104644400-104648600	Weak transcription	Aorta	Aorta
21	chr7:104644400-104649000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr7:104644600-104647800	Weak transcription	Gastric	stomach
23	chr7:104644600-104648600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:104644600-104649200	Genic enhancers	NHEK	skin
25	chr7:104644600-104650200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:104644800-104647000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:104644800-104647600	Enhancers	Primary T cells from cord blood	blood
28	chr7:104644800-104650200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:104644800-104650400	Weak transcription	HSMMtube	muscle
30	chr7:104645000-104647000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr7:104645000-104647000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr7:104645000-104647000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr7:104645000-104647200	Weak transcription	Brain Germinal Matrix	brain
34	chr7:104645000-104647400	Weak transcription	Fetal Brain Male	brain
35	chr7:104645000-104647600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:104645000-104647800	Weak transcription	Colonic Mucosa	Colon
37	chr7:104645000-104648600	Weak transcription	NH-A	brain
38	chr7:104645000-104648800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr7:104645000-104649200	Weak transcription	Fetal Brain Female	brain
40	chr7:104645200-104647600	Weak transcription	Fetal Muscle Leg	muscle
41	chr7:104645200-104648200	Strong transcription	Fetal Stomach	stomach
42	chr7:104645200-104648600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr7:104645200-104650200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:104645400-104647000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:104645400-104647200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr7:104645400-104647400	Weak transcription	Fetal Heart	heart
47	chr7:104645400-104647400	Weak transcription	Small Intestine	intestine
48	chr7:104645400-104647600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:104645400-104647600	Weak transcription	Hela-S3	cervix
50	chr7:104645400-104649400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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