Variant report

Variant	rs7977742
Chromosome Location	chr12:51130207-51130208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51128569..51131031-chr12:51157006..51160452,4	MCF-7	breast:
2	chr12:51128503..51131491-chr12:51131900..51134268,2	K562	blood:
3	chr12:51126340..51128036-chr12:51129957..51132479,2	K562	blood:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10747586	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap]
rs1109726	0.85[AMR][1000 genomes]
rs11609506	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11609941	0.85[AMR][1000 genomes]
rs11832315	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs1345538	1.00[CHB][hapmap]
rs1521516	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap]
rs2250751	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2250752	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2251024	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2251603	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2252589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2554862	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs2684889	0.96[CEU][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2684898	0.82[EUR][1000 genomes]
rs2684900	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs2684901	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2700479	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2700480	0.96[CEU][hapmap];0.90[YRI][hapmap]
rs2700482	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2700485	0.96[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2731434	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2731439	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2731440	0.95[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2731442	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2731443	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57602501	0.82[AMR][1000 genomes]
rs57729468	0.85[AMR][1000 genomes]
rs6580769	0.84[AMR][1000 genomes]
rs66838741	0.84[AMR][1000 genomes]
rs66947035	0.85[AMR][1000 genomes]
rs67218241	0.82[AMR][1000 genomes]
rs67356137	0.85[AMR][1000 genomes]
rs67934435	0.83[AMR][1000 genomes]
rs7305655	0.96[CEU][hapmap];0.95[YRI][hapmap]
rs7307788	0.85[AMR][1000 genomes]
rs7308872	0.81[EUR][1000 genomes]
rs7958114	0.81[AMR][1000 genomes]
rs7960015	0.82[AMR][1000 genomes]
rs7968440	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7977064	0.81[AMR][1000 genomes]
rs7977690	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7978559	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs7979165	1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs829112	1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs829114	0.84[AMR][1000 genomes]
rs829115	0.84[AMR][1000 genomes]
rs861204	1.00[CHB][hapmap]
rs865489	0.85[AMR][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7977742	KIAA1463	cis	multi-tissue	Pritchard
rs7977742	LASS5	cis	cerebellum	SCAN
rs7977742	LASS5	cis	parietal	SCAN
rs7977742	CERS5	cis	Nerve Tibial	GTEx
rs7977742	MCRS1	cis	parietal	SCAN
rs7977742	LASS5	cis	multi-tissue	Pritchard
rs7977742	DIP2B	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51063200-51138600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr12:51063600-51138800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr12:51063600-51145400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:51067400-51143600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:51067600-51142200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:51068200-51141200	Strong transcription	Placenta	Placenta
7	chr12:51068200-51144000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:51074600-51139600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:51080200-51145400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:51086200-51140800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:51086200-51142600	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:51090400-51145400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:51090600-51138400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:51096000-51142000	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:51096200-51144600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:51101000-51144800	Strong transcription	Fetal Stomach	stomach
17	chr12:51105400-51133600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:51108200-51142200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:51110600-51141200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:51110600-51144800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr12:51110800-51142200	Strong transcription	Lung	lung
22	chr12:51111400-51141600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:51111400-51141800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:51111400-51144600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:51111600-51142200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr12:51111800-51136600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:51112000-51141800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:51112000-51142000	Strong transcription	Dnd41	blood
29	chr12:51112000-51144800	Strong transcription	Primary T cells from cord blood	blood
30	chr12:51112200-51144800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr12:51114200-51144800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:51114800-51141800	Strong transcription	HepG2	liver
33	chr12:51114800-51142400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr12:51116200-51140200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr12:51116200-51144000	Strong transcription	Fetal Intestine Large	intestine
36	chr12:51116800-51144000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr12:51116800-51144800	Strong transcription	Primary B cells from cord blood	blood
38	chr12:51117200-51131200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr12:51118200-51143600	Strong transcription	Adipose Nuclei	Adipose
40	chr12:51118800-51133400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:51119000-51139000	Strong transcription	Brain Substantia Nigra	brain
42	chr12:51119200-51130800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:51119200-51144600	Strong transcription	Liver	Liver
44	chr12:51120200-51140400	Strong transcription	Fetal Intestine Small	intestine
45	chr12:51120800-51139000	Strong transcription	Colonic Mucosa	Colon
46	chr12:51120800-51145400	Strong transcription	Fetal Thymus	thymus
47	chr12:51121000-51139000	Strong transcription	Spleen	Spleen
48	chr12:51121000-51140200	Strong transcription	Left Ventricle	heart
49	chr12:51121400-51142200	Strong transcription	GM12878-XiMat	blood
50	chr12:51121400-51145400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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