Variant report

Variant	rs11971935
Chromosome Location	chr7:127422539-127422540
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127415404..127418841-chr7:127421923..127425152,3	K562	blood:
2	chr7:127410218..127412934-chr7:127422329..127425135,2	MCF-7	breast:
3	chr7:127422115..127423719-chr7:127427243..127429540,2	MCF-7	breast:
4	chr7:127418258..127422061-chr7:127422146..127424884,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FSCN3-6	chr7:127422538-127422901	expReg_chr7_9307_+

Extended variants
information (count: 108 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10215276	0.89[ASN][1000 genomes]
rs10251423	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10251548	0.89[EUR][1000 genomes]
rs10255861	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10260037	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1029927	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1075206	0.81[ASN][1000 genomes]
rs10954163	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11521053	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972774	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976841	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11976946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11977012	0.85[ASN][1000 genomes]
rs11977915	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11980318	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12531440	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533846	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539728	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540865	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13237048	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246200	0.88[YRI][hapmap]
rs1362268	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs141450	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419969	0.83[ASN][1000 genomes]
rs16885524	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17151241	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151270	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151466	0.83[ASW][hapmap];0.94[YRI][hapmap]
rs17716738	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17718395	0.96[ASN][1000 genomes]
rs1860934	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1881084	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2014583	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2016786	0.96[EUR][1000 genomes]
rs2043982	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2119452	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2119453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2141259	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2402866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2402867	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2402870	0.96[EUR][1000 genomes]
rs325440	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325442	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325444	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325445	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325446	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325447	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325451	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs327518	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs35121681	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35176520	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35940771	0.96[EUR][1000 genomes]
rs35971861	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779529	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3779530	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808073	1.00[JPT][hapmap]
rs3808087	0.83[ASN][1000 genomes]
rs3808092	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808093	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808095	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808097	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808105	0.85[ASN][1000 genomes]
rs3808106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3808107	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3808112	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3824000	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3824006	0.87[CHD][hapmap]
rs41464647	0.81[ASW][hapmap]
rs4728077	0.85[ASN][1000 genomes]
rs4731376	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4731378	0.96[EUR][1000 genomes]
rs55694225	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56306023	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58583807	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467145	0.96[EUR][1000 genomes]
rs6948493	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6961381	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963455	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963614	1.00[JPT][hapmap]
rs6968199	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969880	0.91[EUR][1000 genomes]
rs712712	0.91[EUR][1000 genomes]
rs712716	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs73234861	0.85[ASN][1000 genomes]
rs73234862	0.85[ASN][1000 genomes]
rs73234880	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73234882	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73234897	0.96[ASN][1000 genomes]
rs73234901	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs741599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs759843	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7785050	0.91[EUR][1000 genomes]
rs7786041	0.89[ASN][1000 genomes]
rs7797663	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7799882	0.96[EUR][1000 genomes]
rs887745	1.00[JPT][hapmap]
rs917831	1.00[JPT][hapmap]
rs917832	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs918793	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972088	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs972089	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs972090	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1030387	chr7:127348973-127455890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11971935	LRRC4	cis	parietal	SCAN
rs11971935	HYAL4	cis	cerebellum	SCAN
rs11971935	SND1	cis	parietal	SCAN
rs11971935	GPR37	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127379200-127437400	Weak transcription	Fetal Stomach	stomach
2	chr7:127382000-127473000	Weak transcription	Hela-S3	cervix
3	chr7:127393200-127422800	Weak transcription	Fetal Thymus	thymus
4	chr7:127395800-127437200	Weak transcription	Fetal Muscle Leg	muscle
5	chr7:127401000-127427000	Weak transcription	HepG2	liver
6	chr7:127401000-127447600	Weak transcription	Fetal Intestine Large	intestine
7	chr7:127401000-127447800	Weak transcription	Fetal Intestine Small	intestine
8	chr7:127403800-127433400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:127407400-127439200	Weak transcription	Primary T cells from cord blood	blood
10	chr7:127407400-127447600	Weak transcription	Dnd41	blood
11	chr7:127407600-127428800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:127408400-127426400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr7:127409400-127430200	Weak transcription	Liver	Liver
14	chr7:127410200-127425000	Weak transcription	Ovary	ovary
15	chr7:127410200-127432800	Weak transcription	Psoas Muscle	Psoas
16	chr7:127411400-127422600	Weak transcription	Pancreas	Pancrea
17	chr7:127411400-127437200	Weak transcription	Left Ventricle	heart
18	chr7:127414600-127427200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr7:127416800-127423200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:127417400-127422600	Weak transcription	NHEK	skin
21	chr7:127418000-127422600	Weak transcription	NH-A	brain
22	chr7:127418000-127427400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:127418200-127426000	Weak transcription	HSMMtube	muscle
24	chr7:127419000-127422600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:127419000-127422600	Weak transcription	HSMM	muscle
26	chr7:127419200-127422600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr7:127419400-127422800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:127419400-127423400	Enhancers	Brain Substantia Nigra	brain
29	chr7:127419800-127422800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:127419800-127423200	Enhancers	Brain Anterior Caudate	brain
31	chr7:127419800-127423600	Enhancers	Brain Cingulate Gyrus	brain
32	chr7:127419800-127435200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr7:127420400-127423000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:127420400-127423400	Enhancers	Brain Hippocampus Middle	brain
35	chr7:127421000-127423200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr7:127421000-127423400	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr7:127421000-127423600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr7:127421000-127423600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr7:127421000-127423800	Enhancers	Primary hematopoietic stem cells	blood
40	chr7:127421200-127423200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr7:127421600-127423000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr7:127421600-127423400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr7:127421800-127423400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:127421800-127423400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:127421800-127423400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:127421800-127423600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:127422000-127423000	Enhancers	Fetal Heart	heart
48	chr7:127422000-127423000	Enhancers	Small Intestine	intestine
49	chr7:127422000-127423000	Enhancers	A549	lung
50	chr7:127422000-127423200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links