Variant report

Variant	rs4972535
Chromosome Location	chr2:174072380-174072381
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	chr2:173939894..173941691-chr2:174070697..174073381,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP3-3	chr2:174072275-174072386	ENSG00000238133.2
2	lnc-SP3-3	chr2:174072275-174072386	ENSG00000238133.2
3	lnc-SP3-3	chr2:174072275-174072387	NONHSAT075529
4	lnc-SP3-3	chr2:174072275-174072386	NR_033882

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10173050	0.82[AFR][1000 genomes]
rs10181133	0.84[CEU][hapmap];0.95[YRI][hapmap]
rs10198981	0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11249	0.82[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs11677913	0.85[YRI][hapmap]
rs11887008	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs11897681	0.83[CEU][hapmap];0.95[YRI][hapmap]
rs12693017	0.84[AFR][1000 genomes]
rs13034748	0.83[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13035366	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs13313780	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13385996	0.84[CEU][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13430550	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13430650	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1439977	0.86[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs16861393	0.82[CHB][hapmap];0.87[CHD][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs1866632	0.82[AFR][1000 genomes]
rs1866633	0.86[AFR][1000 genomes]
rs1866634	0.84[CEU][hapmap];0.95[YRI][hapmap];0.86[EUR][1000 genomes]
rs2289396	0.84[LWK][hapmap];0.82[YRI][hapmap]
rs2289398	0.84[AFR][1000 genomes]
rs2358087	0.85[ASW][hapmap];0.83[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2358089	0.95[ASN][1000 genomes]
rs3769165	0.85[ASW][hapmap];0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769174	0.83[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3769177	0.83[CEU][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4972399	0.82[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs4972536	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs6734666	0.95[YRI][hapmap]
rs7566372	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
2	chr2:174046400-174075800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:174048600-174095200	Weak transcription	Thymus	Thymus
4	chr2:174049200-174083200	Weak transcription	Small Intestine	intestine
5	chr2:174049400-174078200	Weak transcription	HUVEC	blood vessel
6	chr2:174049600-174074400	Weak transcription	Fetal Stomach	stomach
7	chr2:174049600-174079800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:174053400-174075600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:174053400-174078400	Weak transcription	Gastric	stomach
10	chr2:174053400-174082000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:174053400-174089800	Weak transcription	Pancreas	Pancrea
12	chr2:174057400-174075800	Weak transcription	Hela-S3	cervix
13	chr2:174058000-174112800	Weak transcription	Spleen	Spleen
14	chr2:174059000-174075000	Weak transcription	NHLF	lung
15	chr2:174060000-174075200	Weak transcription	Fetal Kidney	kidney
16	chr2:174060200-174092600	Weak transcription	Aorta	Aorta
17	chr2:174061000-174082000	Weak transcription	Fetal Brain Female	brain
18	chr2:174061200-174097600	Weak transcription	Lung	lung
19	chr2:174061400-174092200	Weak transcription	Brain Substantia Nigra	brain
20	chr2:174061600-174074600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:174061600-174077000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:174061600-174083200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:174061600-174083200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:174061800-174072600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:174061800-174075200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:174061800-174080200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:174063200-174074400	Weak transcription	Psoas Muscle	Psoas
28	chr2:174063600-174074400	Weak transcription	Left Ventricle	heart
29	chr2:174063600-174075200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:174063600-174097600	Weak transcription	HSMM	muscle
31	chr2:174063800-174075000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:174063800-174075000	Weak transcription	NH-A	brain
33	chr2:174063800-174076200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:174063800-174081600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:174063800-174083200	Weak transcription	GM12878-XiMat	blood
36	chr2:174063800-174095000	Weak transcription	Right Ventricle	heart
37	chr2:174064200-174074200	Weak transcription	K562	blood
38	chr2:174064200-174074600	Weak transcription	Liver	Liver
39	chr2:174064200-174074600	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:174064200-174082800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:174064200-174083000	Weak transcription	HepG2	liver
42	chr2:174064200-174083400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:174064200-174097600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:174064600-174082000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:174064600-174083200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:174066800-174075000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:174069400-174073800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:174069400-174074200	Weak transcription	A549	lung
49	chr2:174069400-174074400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:174069400-174076000	Weak transcription	Fetal Intestine Large	intestine

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