Variant report

Variant	rs2237342
Chromosome Location	chr7:27796242-27796243
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27793093..27795415-chr7:27795434..27796969,2	K562	blood:
2	chr7:27786993..27792954-chr7:27793164..27797918,6	K562	blood:
3	chr7:27780417..27784283-chr7:27794073..27796581,3	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12164139	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs1524530	0.92[CEU][hapmap]
rs1524531	0.92[CEU][hapmap]
rs17155702	0.84[ASW][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap]
rs3823946	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62449639	0.91[AFR][1000 genomes]
rs6946075	0.92[CEU][hapmap]
rs6961429	0.92[CEU][hapmap];0.88[TSI][hapmap]
rs723699	0.92[CEU][hapmap]
rs723700	0.92[CEU][hapmap]
rs7455882	0.92[CEU][hapmap]
rs7794292	0.92[CEU][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2237342	SNX10	cis	cerebellum	SCAN
rs2237342	TAX1BP1	cis	multi-tissue	Pritchard
rs2237342	HOXA3	cis	cerebellum	SCAN
rs2237342	SCRN1	cis	cerebellum	SCAN
rs2237342	TAX1BP1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27780800-27796400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:27780800-27805600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:27780800-27810200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:27780800-27815200	Weak transcription	Gastric	stomach
5	chr7:27781000-27800200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:27781000-27861800	Weak transcription	Aorta	Aorta
7	chr7:27781400-27799600	Weak transcription	Fetal Stomach	stomach
8	chr7:27781400-27803200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:27781400-27812800	Weak transcription	Brain Germinal Matrix	brain
10	chr7:27784800-27799200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:27784800-27801000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:27784800-27834000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:27784800-27878400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:27785000-27805600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:27785000-27806200	Weak transcription	Spleen	Spleen
16	chr7:27785000-27825000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:27785200-27809800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:27787000-27804200	Weak transcription	Fetal Intestine Small	intestine
19	chr7:27787400-27799200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:27787600-27805600	Weak transcription	Pancreas	Pancrea
21	chr7:27787600-27825000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:27787800-27826600	Weak transcription	Small Intestine	intestine
23	chr7:27788200-27798800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:27788200-27799400	Strong transcription	Dnd41	blood
25	chr7:27788200-27800400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr7:27788200-27801600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:27788200-27801800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:27788200-27801800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr7:27788200-27802200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr7:27788400-27801800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:27789000-27800800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:27789000-27801200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:27789600-27811000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr7:27789800-27805400	Weak transcription	Esophagus	oesophagus
35	chr7:27790200-27815200	Weak transcription	Psoas Muscle	Psoas
36	chr7:27790600-27798600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:27790600-27801000	Weak transcription	Fetal Brain Female	brain
38	chr7:27790600-27825000	Weak transcription	NHLF	lung
39	chr7:27790600-27835000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:27790600-27857400	Weak transcription	Colonic Mucosa	Colon
41	chr7:27790800-27800600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr7:27791000-27797600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr7:27791000-27805400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr7:27791400-27799600	Weak transcription	Fetal Muscle Leg	muscle
45	chr7:27791600-27797600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:27791600-27810000	Weak transcription	Colon Smooth Muscle	Colon
47	chr7:27791800-27805400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr7:27792000-27796600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr7:27792000-27797000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:27792000-27797400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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