Variant report

Variant	rs6446627
Chromosome Location	chr4:7830974-7830975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7828803..7835270-chr4:7836618..7840776,8	K562	blood:
2	chr4:7828718..7832914-chr4:7842245..7845071,3	K562	blood:
3	chr4:7817490..7819833-chr4:7830199..7832039,2	K562	blood:
4	chr4:7817490..7820534-chr4:7830199..7832039,3	K562	blood:
5	chr4:7825242..7828581-chr4:7828624..7832177,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SORCS2-3	chr4:7824831-7831552	refGeneNc_1113_NR_026892

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10049998	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.82[ASN][1000 genomes]
rs11932843	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs11941290	0.86[MEX][hapmap]
rs12639946	0.90[CEU][hapmap]
rs13115701	0.88[ASN][1000 genomes]
rs13131154	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs13137140	0.88[ASN][1000 genomes]
rs13140004	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs13145572	0.88[ASN][1000 genomes]
rs13146302	0.88[ASN][1000 genomes]
rs13147998	0.82[ASN][1000 genomes]
rs1320073	0.88[ASN][1000 genomes]
rs13435273	0.82[ASN][1000 genomes]
rs17770147	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs17770177	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2067842	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2385902	0.88[CHB][hapmap]
rs28394221	0.88[ASN][1000 genomes]
rs28539821	0.88[ASN][1000 genomes]
rs28546404	0.88[ASN][1000 genomes]
rs28605531	0.88[ASN][1000 genomes]
rs28613311	0.84[ASN][1000 genomes]
rs28631977	0.83[ASN][1000 genomes]
rs28673208	0.88[ASN][1000 genomes]
rs28688265	0.88[ASN][1000 genomes]
rs28754920	0.88[ASN][1000 genomes]
rs2891927	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs34072304	0.83[ASN][1000 genomes]
rs34075381	0.88[ASN][1000 genomes]
rs34092549	0.88[ASN][1000 genomes]
rs34119140	0.83[ASN][1000 genomes]
rs34121576	0.88[ASN][1000 genomes]
rs34132874	0.83[ASN][1000 genomes]
rs34181918	0.88[ASN][1000 genomes]
rs34189407	0.88[ASN][1000 genomes]
rs34221000	0.88[ASN][1000 genomes]
rs34383852	0.88[ASN][1000 genomes]
rs34392913	0.88[ASN][1000 genomes]
rs34570748	0.87[ASN][1000 genomes]
rs34598003	0.83[ASN][1000 genomes]
rs34652148	0.88[ASN][1000 genomes]
rs34712341	0.88[ASN][1000 genomes]
rs34868842	0.88[ASN][1000 genomes]
rs34909423	0.83[ASN][1000 genomes]
rs34982807	0.83[ASN][1000 genomes]
rs35138920	0.88[ASN][1000 genomes]
rs35152796	0.88[ASN][1000 genomes]
rs35154266	0.88[ASN][1000 genomes]
rs35238070	0.88[ASN][1000 genomes]
rs35349192	0.88[ASN][1000 genomes]
rs35502845	0.88[ASN][1000 genomes]
rs35727635	0.88[ASN][1000 genomes]
rs35735994	0.88[ASN][1000 genomes]
rs35881667	0.87[ASN][1000 genomes]
rs35905776	0.88[ASN][1000 genomes]
rs35933973	0.81[ASN][1000 genomes]
rs35967175	0.88[ASN][1000 genomes]
rs36013696	0.88[ASN][1000 genomes]
rs36046241	0.84[ASN][1000 genomes]
rs36106793	0.88[ASN][1000 genomes]
rs3934540	0.90[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234831	0.90[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4256209	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs4296663	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs4361385	0.89[CHB][hapmap];0.84[JPT][hapmap];0.91[MKK][hapmap];0.83[ASN][1000 genomes]
rs4411970	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs4443285	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4447865	0.90[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4487321	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs4579115	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4689860	0.80[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs4689865	0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4689875	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696742	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4696747	0.87[ASN][1000 genomes]
rs4696762	0.88[ASN][1000 genomes]
rs4696772	1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.84[ASN][1000 genomes]
rs62289341	0.85[ASN][1000 genomes]
rs62289351	0.85[ASN][1000 genomes]
rs6446624	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446625	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824266	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs6826598	0.84[ASN][1000 genomes]
rs6828574	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs6829505	0.88[ASN][1000 genomes]
rs6829710	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6832352	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.88[ASN][1000 genomes]
rs6833054	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs6837845	0.88[ASN][1000 genomes]
rs6838055	0.88[ASN][1000 genomes]
rs6845014	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs6855982	0.88[ASN][1000 genomes]
rs6856371	0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6856795	0.88[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs71600561	0.84[ASN][1000 genomes]
rs71601887	0.88[ASN][1000 genomes]
rs71601888	0.88[ASN][1000 genomes]
rs71601889	0.88[ASN][1000 genomes]
rs71601890	0.88[ASN][1000 genomes]
rs71601892	0.88[ASN][1000 genomes]
rs7660568	0.88[ASN][1000 genomes]
rs7672185	0.82[EUR][1000 genomes]
rs7682202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682611	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684718	0.84[JPT][hapmap]
rs7691386	0.88[ASN][1000 genomes]
rs7694106	0.83[ASN][1000 genomes]
rs7697255	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.88[ASN][1000 genomes]
rs9996019	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active 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	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
6	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv522369	chr4:7826824-7831977	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6446627	MSX1	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7819800-7834400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:7821200-7859000	Weak transcription	Aorta	Aorta
3	chr4:7824600-7834600	Genic enhancers	HUVEC	blood vessel
4	chr4:7825400-7839400	Weak transcription	Pancreas	Pancrea
5	chr4:7825600-7852200	Weak transcription	Gastric	stomach
6	chr4:7825800-7854200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:7826000-7846000	Weak transcription	Stomach Mucosa	stomach
8	chr4:7826400-7833600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:7826600-7842400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:7826800-7831200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:7827000-7831400	Weak transcription	HepG2	liver
12	chr4:7827600-7832400	Genic enhancers	Fetal Muscle Leg	muscle
13	chr4:7827800-7831000	Genic enhancers	Fetal Stomach	stomach
14	chr4:7828000-7832400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
15	chr4:7828200-7831000	Strong transcription	Brain Germinal Matrix	brain
16	chr4:7828800-7833000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr4:7828800-7833600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:7829000-7834200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr4:7829200-7833400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr4:7829400-7831000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:7829400-7831400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:7829400-7831600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr4:7829400-7831600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr4:7829400-7832000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:7829400-7832200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr4:7829400-7832400	Genic enhancers	HSMM	muscle
27	chr4:7829400-7833400	Genic enhancers	Muscle Satellite Cultured Cells	--
28	chr4:7829400-7834200	Genic enhancers	NH-A	brain
29	chr4:7829600-7831000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:7829800-7831000	Strong transcription	Fetal Brain Female	brain
31	chr4:7829800-7831200	Enhancers	Right Atrium	heart
32	chr4:7829800-7832200	Enhancers	Primary T cells from cord blood	blood
33	chr4:7829800-7832400	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr4:7829800-7832800	Enhancers	Fetal Heart	heart
35	chr4:7830000-7831000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
36	chr4:7830000-7831400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:7830200-7831000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr4:7830200-7831400	Genic enhancers	A549	lung
39	chr4:7830200-7831600	Enhancers	NHDF-Ad	bronchial
40	chr4:7830200-7831800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr4:7830200-7832800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:7830200-7833400	Enhancers	NHLF	lung
43	chr4:7830400-7831200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr4:7830400-7831200	Enhancers	HMEC	breast
45	chr4:7830400-7832400	Weak transcription	Lung	lung
46	chr4:7830400-7832600	Enhancers	Small Intestine	intestine
47	chr4:7830400-7832800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr4:7830400-7833000	Enhancers	K562	blood
49	chr4:7830400-7834200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:7830400-7844200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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